Initial commit.

.gitignore

@@ -21,3 +21,4 @@
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*
+/target/

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 Azeem
+Copyright (c) 2015 Azeem
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,2 +1,22 @@
-# ssic
-Sequence Similarity and Identity Calculator (DNA + Protein)
+# ![icon](icon.png) SSIC (Sequence Similarity and Identity Calculator)
+
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg?style=flat-square)](https://github.com/iamAzeem/ssic/blob/master/LICENSE)
+
+SSIC is a global alignment tool to calculate the similarity and identity of DNA and protein sequences.
+
+## Depedencies
+
+* Java
+* BioJava (3.1.0)
+  * biojava3-core
+  * biojava3-alignment
+* Maven
+
+## Demo
+
+![demo](demo.gif)
+
+## Contact
+
+Email: azeem.sajid@gmail.com  
+LinkedIn: https://www.linkedin.com/in/az33msajid/

pom.xml

@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" 
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>com</groupId>
+    <artifactId>SSIC</artifactId>
+    <version>1.0.0</version>
+    <packaging>jar</packaging>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <maven.compiler.source>11</maven.compiler.source>
+        <maven.compiler.target>11</maven.compiler.target>
+    </properties>
+
+    <build>    
+        <plugins>
+            <plugin>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>single</goal>
+                        </goals>
+                    </execution>
+                </executions>
+                <configuration>
+                    <archive>
+                        <manifest>
+                            <addClasspath>true</addClasspath>
+                            <mainClass>ssic.SSIC</mainClass>
+                        </manifest>
+                    </archive>
+                    <descriptorRefs>
+                        <descriptorRef>jar-with-dependencies</descriptorRef>
+                    </descriptorRefs>
+                    <appendAssemblyId>false</appendAssemblyId>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+
+    <repositories>
+        <repository>
+            <id>biojava-legacy-repo</id>
+            <name>BioJava's Git based legacy maven repo</name>
+            <url>https://github.com/biojava/maven-repo/raw/master/</url>
+        </repository>
+    </repositories>
+
+    <dependencies>
+      <dependency>
+        <groupId>org.biojava</groupId>
+        <artifactId>biojava3-core</artifactId>
+        <version>3.1.0</version>
+      </dependency>
+      <dependency>
+        <groupId>org.biojava</groupId>
+        <artifactId>biojava3-alignment</artifactId>
+        <version>3.1.0</version>
+      </dependency>
+    </dependencies>
+</project>

src/main/java/ssic/AboutPanel.java

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+package ssic;
+
+import java.awt.*;
+import javax.swing.*;
+
+@SuppressWarnings( "serial" )
+public final class AboutPanel extends JPanel
+{
+    private final String fontName = "Courier New";
+
+    private JLabel lblTitle;
+    private JLabel lblVersion;
+    private JLabel lblIcon;
+    private JLabel lblAuthor;
+    private JLabel lblEmail;
+
+    public AboutPanel()
+    {
+        initComponents();
+    }
+
+    private void initComponents()
+    {
+        setLayout( new FlowLayout() );
+
+        final String title   = "Sequence Similarity and Identity Calculator (SSIC)";
+        final String version = "Version: 1.0.0";
+        final String author  = "Developed by: AZEEM";
+        final String email   = "Email: azeem.sajid@gmail.com";
+
+        final int CENTER = SwingConstants.CENTER;
+
+        lblTitle   = new JLabel( title, CENTER );
+        lblVersion = new JLabel( version, CENTER );
+        lblIcon    = new JLabel( "", CENTER );
+        lblAuthor  = new JLabel( author, CENTER );
+        lblEmail   = new JLabel( email, CENTER );
+
+        lblTitle.setPreferredSize( SIZE(792, 130) );
+        lblTitle.setFont( FONT(22) );
+
+        lblVersion.setPreferredSize( SIZE(792, 10) );
+        lblVersion.setFont( FONT(18) );
+
+        lblIcon.setPreferredSize( SIZE(792, 80) );
+        lblIcon.setIcon( new ImageIcon(getClass().getClassLoader().getResource(Defaults.WIN_ICON)) );
+
+        lblAuthor.setPreferredSize( SIZE(792, 200) );
+        lblAuthor.setFont( FONT(22) );
+
+        lblEmail.setPreferredSize( SIZE(792, 30) );
+        lblEmail.setFont( FONT(20) );
+
+        add( lblTitle );
+        add( lblVersion );
+        add( lblAuthor );
+        add( lblEmail );
+    }
+
+    private Dimension SIZE( final int width, final int height )
+    {
+        return new Dimension(width, height);
+    }
+
+    private Font FONT( final int size )
+    {
+        return new Font(fontName, Font.BOLD, size);
+    }
+}

src/main/java/ssic/Alignment.java

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+package ssic;
+
+public final class Alignment
+{
+    private final String querySequence;
+    private final String targetSequence;
+    private final String similarity;
+    private final String identity;
+    private final String alignmentType;
+    private final String alignmentAsString;
+
+    public Alignment( final String _querySequence,
+                      final String _targetSequence,
+                      final String _similarity,
+                      final String _identity,
+                      final String _alignmentType,
+                      final String _alignmentAsString )
+    {
+        querySequence     = _querySequence;
+        targetSequence    = _targetSequence;
+        similarity        = _similarity;
+        identity          = _identity;
+        alignmentType     = _alignmentType;
+        alignmentAsString = _alignmentAsString;
+    }
+
+    public final String getTitle()
+    {
+        String s;
+        s  = getQuerySequenceName()  + " vs. " + getTargetSequenceName();
+        s += ", Similarity: " + getSimilarity();
+        s += ", Identity: "   + getIdentity();
+        s += ", Type: "       + getAlignmentType();
+        return s;
+    }
+
+    public final String getQuerySequenceName()
+    {
+        return querySequence;
+    }
+
+    public final String getTargetSequenceName()
+    {
+        return targetSequence;
+    }
+
+    public final String getSimilarity()
+    {
+        return similarity;
+    }
+
+    public final String getIdentity()
+    {
+        return identity;
+    }
+
+    public final String getAlignmentType()
+    {
+        return alignmentType;
+    }
+
+    public final String getAlignmentAsString()
+    {
+        return alignmentAsString;
+    }
+
+    @Override
+    public final String toString()
+    {
+        String s;
+        s  = getQuerySequenceName() + " vs. " + getTargetSequenceName() + "\n\n";
+        s += "Similarity: "         + getSimilarity()                   + "\n";
+        s += "Identity  : "         + getIdentity()                     + "\n";
+        s += "Align Type: "         + getAlignmentType()                + "\n\n";
+        s += "Alignment :\n\n"      + getAlignmentAsString()            + "\n";
+        return s;
+    }
+}