First commit

build.xml

@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- You may freely edit this file. See commented blocks below for -->
+<!-- some examples of how to customize the build. -->
+<!-- (If you delete it and reopen the project it will be recreated.) -->
+<!-- By default, only the Clean and Build commands use this build script. -->
+<!-- Commands such as Run, Debug, and Test only use this build script if -->
+<!-- the Compile on Save feature is turned off for the project. -->
+<!-- You can turn off the Compile on Save (or Deploy on Save) setting -->
+<!-- in the project's Project Properties dialog box.-->
+<project name="RFAM" default="default" basedir=".">
+    <description>Builds, tests, and runs the project RFAM.</description>
+    <import file="nbproject/build-impl.xml"/>
+    <!--
+
+    There exist several targets which are by default empty and which can be 
+    used for execution of your tasks. These targets are usually executed 
+    before and after some main targets. They are: 
+
+      -pre-init:                 called before initialization of project properties
+      -post-init:                called after initialization of project properties
+      -pre-compile:              called before javac compilation
+      -post-compile:             called after javac compilation
+      -pre-compile-single:       called before javac compilation of single file
+      -post-compile-single:      called after javac compilation of single file
+      -pre-compile-test:         called before javac compilation of JUnit tests
+      -post-compile-test:        called after javac compilation of JUnit tests
+      -pre-compile-test-single:  called before javac compilation of single JUnit test
+      -post-compile-test-single: called after javac compilation of single JUunit test
+      -pre-jar:                  called before JAR building
+      -post-jar:                 called after JAR building
+      -post-clean:               called after cleaning build products
+
+    (Targets beginning with '-' are not intended to be called on their own.)
+
+    Example of inserting an obfuscator after compilation could look like this:
+
+        <target name="-post-compile">
+            <obfuscate>
+                <fileset dir="${build.classes.dir}"/>
+            </obfuscate>
+        </target>
+
+    For list of available properties check the imported 
+    nbproject/build-impl.xml file. 
+
+
+    Another way to customize the build is by overriding existing main targets.
+    The targets of interest are: 
+
+      -init-macrodef-javac:     defines macro for javac compilation
+      -init-macrodef-junit:     defines macro for junit execution
+      -init-macrodef-debug:     defines macro for class debugging
+      -init-macrodef-java:      defines macro for class execution
+      -do-jar:                  JAR building
+      run:                      execution of project 
+      -javadoc-build:           Javadoc generation
+      test-report:              JUnit report generation
+
+    An example of overriding the target for project execution could look like this:
+
+        <target name="run" depends="RFAM-impl.jar">
+            <exec dir="bin" executable="launcher.exe">
+                <arg file="${dist.jar}"/>
+            </exec>
+        </target>
+
+    Notice that the overridden target depends on the jar target and not only on 
+    the compile target as the regular run target does. Again, for a list of available 
+    properties which you can use, check the target you are overriding in the
+    nbproject/build-impl.xml file. 
+
+    -->
+</project>

manifest.mf

@@ -0,0 +1,3 @@
+Manifest-Version: 1.0
+X-COMMENT: Main-Class will be added automatically by build
+

nbproject/genfiles.properties

@@ -0,0 +1,8 @@
+build.xml.data.CRC32=c68b23b5
+build.xml.script.CRC32=ef345505
+build.xml.stylesheet.CRC32=8064a381@1.80.1.48
+# This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
+# Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
+nbproject/build-impl.xml.data.CRC32=c68b23b5
+nbproject/build-impl.xml.script.CRC32=eb5a1d57
+nbproject/build-impl.xml.stylesheet.CRC32=830a3534@1.80.1.48

nbproject/project.properties

@@ -0,0 +1,81 @@
+annotation.processing.enabled=true
+annotation.processing.enabled.in.editor=false
+annotation.processing.processors.list=
+annotation.processing.run.all.processors=true
+annotation.processing.source.output=${build.generated.sources.dir}/ap-source-output
+application.title=RFAM
+application.vendor=daniil
+build.classes.dir=${build.dir}/classes
+build.classes.excludes=**/*.java,**/*.form
+# This directory is removed when the project is cleaned:
+build.dir=build
+build.generated.dir=${build.dir}/generated
+build.generated.sources.dir=${build.dir}/generated-sources
+# Only compile against the classpath explicitly listed here:
+build.sysclasspath=ignore
+build.test.classes.dir=${build.dir}/test/classes
+build.test.results.dir=${build.dir}/test/results
+# Uncomment to specify the preferred debugger connection transport:
+#debug.transport=dt_socket
+debug.classpath=\
+    ${run.classpath}
+debug.test.classpath=\
+    ${run.test.classpath}
+# Files in build.classes.dir which should be excluded from distribution jar
+dist.archive.excludes=
+# This directory is removed when the project is cleaned:
+dist.dir=dist
+dist.jar=${dist.dir}/RFAM.jar
+dist.javadoc.dir=${dist.dir}/javadoc
+endorsed.classpath=
+excludes=
+file.reference.mysql-connector-java-5.1.46-bin.jar=/home/daniil/Downloads/mysql-connector-java-5.1.46/mysql-connector-java-5.1.46-bin.jar
+file.reference.mysql-connector-java-5.1.46-bin.jar-1=lib/mysql-connector-java-5.1.46-bin.jar
+includes=**
+jar.compress=false
+javac.classpath=\
+    ${file.reference.mysql-connector-java-5.1.46-bin.jar-1}
+# Space-separated list of extra javac options
+javac.compilerargs=
+javac.deprecation=false
+javac.external.vm=true
+javac.processorpath=\
+    ${javac.classpath}:\
+    ${file.reference.mysql-connector-java-5.1.46-bin.jar}
+javac.source=1.8
+javac.target=1.8
+javac.test.classpath=\
+    ${javac.classpath}:\
+    ${build.classes.dir}:\
+    ${file.reference.mysql-connector-java-5.1.46-bin.jar}
+javac.test.processorpath=\
+    ${javac.test.classpath}
+javadoc.additionalparam=
+javadoc.author=false
+javadoc.encoding=${source.encoding}
+javadoc.noindex=false
+javadoc.nonavbar=false
+javadoc.notree=false
+javadoc.private=false
+javadoc.splitindex=true
+javadoc.use=true
+javadoc.version=false
+javadoc.windowtitle=
+main.class=rfam.DB
+manifest.file=manifest.mf
+meta.inf.dir=${src.dir}/META-INF
+mkdist.disabled=false
+platform.active=default_platform
+run.classpath=\
+    ${javac.classpath}:\
+    ${build.classes.dir}
+# Space-separated list of JVM arguments used when running the project.
+# You may also define separate properties like run-sys-prop.name=value instead of -Dname=value.
+# To set system properties for unit tests define test-sys-prop.name=value:
+run.jvmargs=
+run.test.classpath=\
+    ${javac.test.classpath}:\
+    ${build.test.classes.dir}
+source.encoding=UTF-8
+src.dir=src
+test.src.dir=test

nbproject/project.xml

@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://www.netbeans.org/ns/project/1">
+    <type>org.netbeans.modules.java.j2seproject</type>
+    <configuration>
+        <data xmlns="http://www.netbeans.org/ns/j2se-project/3">
+            <name>RFAM</name>
+            <source-roots>
+                <root id="src.dir"/>
+            </source-roots>
+            <test-roots>
+                <root id="test.src.dir"/>
+            </test-roots>
+        </data>
+    </configuration>
+</project>

src/rfam/DB.java

@@ -0,0 +1,53 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam;
+
+import rfam.RFAMWrapper.RFAMFilter;
+import rfam.RFAMWrapper.RFAMFilteredTable;
+import rfam.RFAMWrapper.RFAMTable;
+import rfam.RFAMWrapper.RFAMTableStats;
+import rfam.RFAMWrapper.RFAMColumnStats;
+import rfam.RFAMWrapper.RFAMWrapper;
+import java.sql.SQLException;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import rfam.RFAMWrapper.RFAMColumnFilteredStats;
+
+/**
+ *
+ * @author daniil
+ */
+public class DB {
+
+    /**
+     * @param args the command line arguments
+     */
+    public static void main(String[] args) {
+        try {
+            RFAMWrapper wrapper = new RFAMWrapper();
+            
+            RFAMTable table = new RFAMTable(wrapper, "family");
+            RFAMFilteredTable filteredTable = new RFAMFilteredTable(table);
+            
+            RFAMTableStats tableStats = new RFAMTableStats(filteredTable);
+            RFAMColumnStats columnStats = new RFAMColumnStats(tableStats, "description");
+            
+            RFAMColumnFilteredStats charStats = new RFAMColumnFilteredStats(columnStats);
+            
+            filteredTable.applyFilter(new RFAMFilter("author").equals("Moxon SJ"));
+            filteredTable.applyFilter(new RFAMFilter("description").contains(' '));
+            
+            charStats.applyFilter(new RFAMFilter().contains('a'));
+            
+            System.out.println(String.format("Total char count: %d", columnStats.getCharCount()));
+            System.out.println(String.format("Occurences of char 'a': %d", charStats.getCharCount()));
+            System.out.println(String.format("Percentage of occurences of char 'a': %f", charStats.getCharPercentage()));
+        } catch (ClassNotFoundException | SQLException | IllegalAccessException | InstantiationException ex) {
+            Logger.getLogger(DB.class.getName()).log(Level.SEVERE, null, ex);
+        }
+    }
+    
+}

src/rfam/RFAMWrapper/RFAMColumnFilteredStats.java

@@ -0,0 +1,32 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam.RFAMWrapper;
+
+import java.sql.SQLException;
+import java.util.ArrayList;
+
+/**
+ *
+ * @author daniil
+ */
+public class RFAMColumnFilteredStats implements RFAMColumnStatsInterface {
+    private RFAMColumnStats stats;
+    private ArrayList<RFAMFilter> filters;
+
+    public RFAMColumnFilteredStats(RFAMColumnStats stats) {
+        this.stats = stats;
+    }
+    
+    public void applyFilter(RFAMFilter filter) {
+        filters.add(filter);
+    }
+    public int getCharCount() throws SQLException {
+        return stats.getCharCount(filters);
+    }
+    public double getCharPercentage() throws SQLException {
+        return stats.getCharCount()*100/stats.getCharCount(filters);
+    }
+}

src/rfam/RFAMWrapper/RFAMColumnStats.java

@@ -0,0 +1,37 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam.RFAMWrapper;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+
+/**
+ *
+ * @author daniil
+ */
+public class RFAMColumnStats implements RFAMColumnStatsInterface {
+    private ResultSet result;
+    private String column;
+    public RFAMColumnStats(RFAMTableStats stats, String column) throws SQLException {
+        this.result = stats.getTable().select(column);
+        this.column = column;
+    }
+    public int getCharCount() throws SQLException {
+        return getCharCount(new ArrayList<RFAMFilter>());
+    }
+    public int getCharCount(ArrayList<RFAMFilter> filters) throws SQLException {
+        int count = 0;
+        String value;
+        while ((value = result.getString(column)) != null) {
+            for (RFAMFilter filter: filters) {
+                count += filter.count(value);
+            }
+        }
+        result.absolute(0);
+        return count;
+    }
+}

src/rfam/RFAMWrapper/RFAMColumnStatsInterface.java

@@ -0,0 +1,16 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam.RFAMWrapper;
+
+import java.sql.SQLException;
+
+/**
+ *
+ * @author daniil
+ */
+public interface RFAMColumnStatsInterface {
+    public int getCharCount() throws SQLException;
+}

src/rfam/RFAMWrapper/RFAMFilter.java

@@ -0,0 +1,107 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam.RFAMWrapper;
+
+import java.util.ArrayList;
+
+/**
+ *
+ * @author daniil
+ */
+public class RFAMFilter {
+    private String column;
+    private ArrayList<String> contains;
+    private ArrayList<String> equals;
+    private Integer index = 0;
+    
+    public RFAMFilter(String column) {
+        this.column = column;
+    }
+    public RFAMFilter() {
+    }
+    
+    public RFAMFilter contains(char filter) {
+        return contains(String.valueOf(filter));
+    }
+    public RFAMFilter contains(String filter) {
+        contains.add(filter);
+        return this;
+    }
+
+    public RFAMFilter equals(char filter) {
+        return equals(String.valueOf(filter));
+    }
+    public RFAMFilter equals(String filter) {
+        equals.add(filter);
+        return this;
+    }
+    
+    public String getColumn() {
+        return column;
+    }
+    public ArrayList<String> getMatchFilters() {
+        return contains;
+    }
+    public ArrayList<String> getEqualFilters() {
+        return equals;
+    }
+    
+    @Override
+    public String toString() {
+        String result = "";
+        String and = "";
+        if (equals.size() > 0) {
+            result += column+" IN (";
+            for (String equal: equals) {
+                result += "?, ";
+            }
+            result += ")";
+            if (contains.size() > 0) {
+                and = " AND ";
+            }
+        }
+        for (String match: contains) {
+            result += and+column+" LIKE %?%";
+            and = " AND ";
+        }
+        return result;
+    }
+    public String getNext() {
+        if (index < contains.size()) {
+            return contains.get(index++);
+        }
+        Integer newindex = index - contains.size();
+        if (newindex < equals.size()) {
+            index = 0;
+            return null;
+        }
+        index++;
+        return equals.get(newindex);
+    }
+    
+    
+    public int count(String value) {
+        if (contains.size() == 0 && equals.size() == 0) {
+            return value.length();
+        }
+        
+        boolean match = false;
+        for (String equal: equals) {
+            match = match || value.equals(equal);
+        }
+        
+        if (!match) {
+            return 0;
+        }
+        
+        int count = 0;
+        for (String contain: contains) {
+            count += value.split(contain).length-1;
+        }
+        
+        return count;
+    }
+}

src/rfam/RFAMWrapper/RFAMFilteredTable.java

@@ -0,0 +1,46 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam.RFAMWrapper;
+
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.ArrayList;
+
+/**
+ *
+ * @author daniil
+ */
+public class RFAMFilteredTable implements RFAMTableInterface {
+    private RFAMTable table;
+    private ArrayList<RFAMFilter> filters;
+    
+    public RFAMFilteredTable(RFAMTable table) {
+        this.table = table;
+    }
+    
+    public void applyFilter(RFAMFilter filter) {
+        filters.add(filter);
+    }
+    public ResultSet select(String field) throws SQLException {
+        return select(new String[] { field });
+    }
+    public ResultSet select(String[] fields) throws SQLException {
+        String whereClause = "";
+        for (RFAMFilter filter: filters) {
+            whereClause += filter;
+        }
+        PreparedStatement statement = table.select(fields, whereClause);
+        Integer index = 0;
+        String parameter;
+        for (RFAMFilter filter: filters) {
+            while ((parameter = filter.getNext()) != null) {
+                statement.setString(index++, parameter);
+            }
+        }
+        return statement.executeQuery();
+    }
+ }

src/rfam/RFAMWrapper/RFAMTable.java

@@ -0,0 +1,35 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam.RFAMWrapper;
+import java.sql.*;
+
+/**
+ *
+ * @author daniil
+ */
+public class RFAMTable implements RFAMTableInterface, RFAMWrapperInterface {
+    private RFAMWrapper wrapper;
+    private String table;
+    public RFAMTable(RFAMWrapper wrapper, String table) {
+        this.wrapper = wrapper;
+        this.table = table;
+    }
+    
+    public RFAMFilteredTable getFilteredTable() {
+        return new RFAMFilteredTable(this);
+    }
+    
+    protected PreparedStatement select(String[] fields, String whereClause) throws SQLException {
+        return wrapper.select(fields, table, whereClause);
+    }
+    public ResultSet select(String[] fields) throws SQLException {
+        return wrapper.select(fields, table);
+    }    
+    public ResultSet select(String field) throws SQLException {
+        return wrapper.select(field, table);
+    }
+
+}

src/rfam/RFAMWrapper/RFAMTableInterface.java

@@ -0,0 +1,18 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam.RFAMWrapper;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+
+/**
+ *
+ * @author daniil
+ */
+public interface RFAMTableInterface {
+    public ResultSet select(String[] fields) throws SQLException;
+    public ResultSet select(String field) throws SQLException;
+}

src/rfam/RFAMWrapper/RFAMTableStats.java

@@ -0,0 +1,25 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam.RFAMWrapper;
+
+import java.sql.SQLException;
+
+/**
+ *
+ * @author daniil
+ */
+public class RFAMTableStats {
+    private RFAMTableInterface table;
+    public RFAMTableStats(RFAMTableInterface table) {
+        this.table = table;
+    }
+    public RFAMTableInterface getTable() {
+        return table;
+    }
+    public RFAMColumnStats getColumn(String column) throws SQLException {
+        return new RFAMColumnStats(this, column);
+    }
+}

src/rfam/RFAMWrapper/RFAMWrapper.java

@@ -0,0 +1,50 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam.RFAMWrapper;
+import java.sql.*;
+
+/**
+ *
+ * @author daniil
+ */
+public class RFAMWrapper implements RFAMWrapperInterface {
+    private final String driver = "com.mysql.jdbc.driver";
+    private final String URL = "jdbc:mysql://mysql-rfam-public.ebi.ac.uk:4497/Rfam";
+    private final String username = "rfamro";
+    private final String password = "";
+    
+    private Connection connection;
+    public RFAMWrapper() throws ClassNotFoundException, SQLException, IllegalAccessException, InstantiationException {
+        Class.forName(driver).newInstance();
+        connection = DriverManager.getConnection(URL, username, password);
+    }
+    
+    public RFAMTable getTable(String table) {
+        return new RFAMTable(this, table);
+    }
+    public RFAMFilteredTable getFilteredTable(String table) {
+        return new RFAMFilteredTable(new RFAMTable(this, table));
+    }
+    
+    protected PreparedStatement select(String field, String fromTable, String whereClause) throws SQLException {
+        return select(new String[] { field }, fromTable, whereClause);
+    }
+    protected PreparedStatement select(String[] fields, String fromTable, String whereClause) throws SQLException {
+        String field = String.join(", ", fields);
+        if (whereClause.length() > 0) {
+            whereClause = " WHERE "+whereClause;
+        }
+        return connection.prepareStatement("SELECT "+field+" FROM "+fromTable+whereClause);
+    }
+    
+    public ResultSet select(String field, String fromTable) throws SQLException {
+        return select(new String[] { field }, fromTable);        
+    }
+    public ResultSet select(String[] fields, String fromTable) throws SQLException {
+        String field = String.join(", ", fields);
+        return connection.prepareStatement("SELECT "+field+" FROM "+fromTable).executeQuery();
+    }
+}

src/rfam/RFAMWrapper/RFAMWrapperInterface.java

@@ -0,0 +1,17 @@
+/*
+ * To change this license header, choose License Headers in Project Properties.
+ * To change this template file, choose Tools | Templates
+ * and open the template in the editor.
+ */
+package rfam.RFAMWrapper;
+
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+
+/**
+ *
+ * @author daniil
+ */
+public interface RFAMWrapperInterface {
+}