alignjframe.java

emboss的linux版本的源代码

    JCheckBoxMenuItem sizeColor  =
               new JCheckBoxMenuItem("Red=Tiny, Green=Small, Blue=Large");
    propertyMenu.add(sizeColor);
    group.add(sizeColor);
    sizeColor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.sizeColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.sizeColor;
        colourScheme("Red=Tiny, Green=Small, Blue=Large");
      }
    });

// other colour schemes
    JCheckBoxMenuItem taylor = new JCheckBoxMenuItem("Taylor Colour");
    viewMenu.add(taylor);
    group.add(taylor);
    taylor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.taylorColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.taylorColor;
        colourScheme("Taylor");
      }
    });

    residueColor = new JCheckBoxMenuItem("Residue Colour");
    viewMenu.add(residueColor);
    group.add(residueColor);
    residueColor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.residueColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.residueColor;
        colourScheme("Residue");
      }
    });

    JCheckBoxMenuItem rasmolColor = new JCheckBoxMenuItem("Rasmol Colour");
    viewMenu.add(rasmolColor);
    group.add(rasmolColor);
    rasmolColor.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.rasmolColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.rasmolColor;
        colourScheme("Rasmol");
      }
    });

    JCheckBoxMenuItem nuc = new JCheckBoxMenuItem("Nucleotide Colour");
    viewMenu.add(nuc);
    group.add(nuc);
    nuc.addActionListener(new ActionListener()
    {
      public void actionPerformed(ActionEvent e)
      {
        gsc.setColorScheme(SequenceProperties.baseColor);
        jspSequence.setViewportView(gsc);
        currentColour = SequenceProperties.baseColor;
        colourScheme("Nucleotide");
      }
    });
    viewMenu.add(new JSeparator());

  }


  /**
  *
  *
  *  red, blue, cyan, darkGray, gray , green, lightGray,
  *  magenta , orange, pink, white, yellow, black
  *
  */
  private static Color resolveColor(String[] args,int index)
  {
    if(args[index].equalsIgnoreCase("red"))
      return Color.red;
    else if(args[index].equalsIgnoreCase("blue"))
      return Color.blue;
    else if(args[index].equalsIgnoreCase("black"))
      return Color.black;
    else if(args[index].equalsIgnoreCase("cyan"))
      return Color.cyan;
    else if(args[index].equalsIgnoreCase("darkGray"))
      return Color.darkGray;
    else if(args[index].equalsIgnoreCase("gray"))
      return Color.gray;
    else if(args[index].equalsIgnoreCase("green"))
      return Color.green;
    else if(args[index].equalsIgnoreCase("lightGray"))
      return Color.lightGray;
    else if(args[index].equalsIgnoreCase("magenta"))
      return Color.magenta;
    else if(args[index].equalsIgnoreCase("orange"))
      return Color.orange;
    else if(args[index].equalsIgnoreCase("pink"))
      return Color.pink;
    else if(args[index].equalsIgnoreCase("white"))
      return Color.white;
    else if(args[index].equalsIgnoreCase("yellow"))
      return Color.yellow;
    else if(args[index].equalsIgnoreCase("black"))
      return Color.black;

    return null;
  }
  
  /**
  *
  * Extends WindowAdapter to close window
  *
  */
  class winExit extends WindowAdapter
  {
     public void windowClosing(WindowEvent we)
     {
        dispose();
     }
  }


  public static void main(String args[])
  {
    AlignJFrame ajFrame = null;

    if( args.length > 0 )
    {
      for(int i=0;i<args.length;i++)
      {
        if(args[i].indexOf("-help") > -1)
        {
          System.out.println(
              "\n                  Jemboss Alignment Editor\n\n"+
              "DESCRIPTION\n"+
              "The Jemboss Alignment Editor can be used interactively to\n"+
              "edit a sequence alignment (read in fasta or MSF format). It can\n"+
              "also be used from the command line to produce image files\n"+
              "of the alignment.\n\nUSAGE\n"+
              "java org/emboss/jemboss/editor/AlignJFrame file [options]\n\n"+
              "file       This is the multiple sequence alignment in\n"+
              "           fasta or MSF format.\n\n"+
              "OPTIONS\n"+
              "-calc      Calculate consensus and display under the alignment.\n"+
              "           The following 3 flags can be used to define values\n"+
              "           used in the calculations.\n"+
              "           -plu       (plurality) minimum positive match score\n"+
              "                      value for there to be a consensus.\n"+
              "           -numid     minimum number of identities for there to\n"+
              "                      be a consensus.\n"+
              "           -case      minimum positive match score for setting\n"+
              "                      the consensus to upper-case.\n"+
              "-color     Used to define a colour scheme, below is the list of\n"+
              "           available colour schemes:\n"+
              "           taylor\n"+
              "           residue\n"+
              "           rasmol\n"+
              "           acid\n"+
              "           polar\n"+
              "           hydrophobic\n"+
              "           aromatic\n"+
              "           surface\n"+
              "           charge\n"+
              "           size\n"+
              "           base\n\n"+
              "       java org.emboss.jemboss.editor.AlignJFrame file -color size\n\n"+
              "-font      Set the font size.\n"+
              "-id        Display a percentage ID pair table.\n"+
              "-noshow    Turns of the alignment display.\n"+
              "-nres      Number of residues to each line is a print out.\n"+
              "-pretty    EMBOSS prettyplot colour scheme. The -matrix flag option\n"+
              "           can be used to define a scoring matrix for identifying\n"+
              "           positive matches.\n"+
              "           -noBox         switch off box drawing around identical and\n"+
              "                          positive matches.\n"+
              "           -minID         define the minimum number of identities. The\n"+
              "                          default for this is the number of sequences\n"+
              "                          in the file.\n"+
              "           -match         define a threshold value for the number of\n"+
              "                          positive matches, the default is half the\n"+
              "                          total wgt.\n"+
              "           -colID         define a lettering colour for the identities.\n"+
              "           -colIDBack     define a background colour for identities.\n"+
              "           -colMatch      define a lettering  colour for positive matches.\n"+  
              "           -colMatchBack  define a background colour for positive\n"+
              "                           matches.\n"+
              "           Available colour options:\n"+  
              "           red, blue, cyan, darkGray, gray , green, lightGray,\n"+
              "           magenta , orange, pink, white, yellow, black\n"+     
              "-print     Print the alignment image. The following 2 flags can be\n"+
              "           used along with the print flag\n"+
              "           -prefix     prefix for image output file.\n"+
              "           -onePage    fit the alignment to one page. This option must be\n"+
              "                       be used with the -nres flag to define the residues\n"+
              "                       per line.\n"+
              "           -type       png or jpeg (default is jpeg).\n"+
              "           -antialias  turn anti-aliasing on.\n"+
              "           -landscape  Print as landscape (the default is portrait).\n"+
              "           -margin     Define the left, right, top and bottom margin\n"+
              "                       (in cm).\n"+
              "       java org.emboss.jemboss.editor.AlignJFrame file -matrix EBLOSUM62 \\\n"+
              "                -noshow -print -margin 0.5 0.5 0.5 0.5\n\n"+
              "-matrix    To define a scoring matrix. Used with the -pretty and -calc\n"+
              "           option.\n"+
              "-list      List the available scoring matrix files.\n\n"+
              "EXAMPLE\n"+
              "java org.emboss.jemboss.editor.AlignJFrame file -matrix EBLOSUM80 \\\n"+
              "                             -pretty -noshow -id -print -type png\n\n"+
              "java org.emboss.jemboss.editor.AlignJFrame file -matrix EPAM250 \\\n"+
              "                -pretty -colIDBack black -colID white -print \\\n"+
              "                -margin 0.5 0.5 0.5 0.0 -noshow\n");
          System.exit(0);
        }
      }

      File seqFile = new File(args[0]);
      if(seqFile.canRead())
      {
        ajFrame = new AlignJFrame(true);
        SequenceReader sr = new SequenceReader(seqFile);
        sr.getSequenceFile();
        ajFrame.openMethod(sr.getSequenceVector());
        ajFrame.setTitle("Jemboss Alignment Viewer    :: "+
                         seqFile.getName());
        gsc.setMatrix(mat);
      }

      String prefix = "output";
      String type   = "jpeg";
      boolean show  = true;
      boolean print = false;
      int nresiduesPerLine = 0;

      float wgt = getTotalWeight(gsc.getSequenceCollection());
      double lmargin = -0.5;  // left margin
      double rmargin = -0.5;  // right margin
      double tmargin = -0.5;  // top margin
      double bmargin = -0.5;  // bottom margin
      float plu = wgt/2.f;
      float cas = wgt/2.f;
      int ident = 0;
      int minID = gsc.getNumberSequences();
      float match = wgt/2.f;
      Color colID        = Color.red;
      Color colMatch     = Color.blue;
      Color colIDBack    = Color.white;
      Color colMatchBack = Color.white;
      boolean prettyBox  = true;
      boolean landscape  = false;
      boolean onePage    = false;
      boolean antialias  = false;

      for(int i=0;i<args.length;i++)
      {
        if(args[i].indexOf("-matrix") > -1)
        {
          mat = new Matrix("resources/resources.jar",
                           args[i+1]);
          gsc.setMatrix(mat);
          statusField.setText("Current matrix: "+args[i+1]);
        }
        else if(args[i].indexOf("-plu") > -1)
          plu = Float.parseFloat(args[i+1]);
        else if(args[i].indexOf("-match") > -1)
          match = Float.parseFloat(args[i+1]);
        else if(args[i].indexOf("-case") > -1)
          cas = Float.parseFloat(args[i+1]);
        else if(args[i].indexOf("-numid") > -1)
          ident = Integer.parseInt(args[i+1]);
        else if(args[i].indexOf("-colIDBack") > -1)
        {
          Color col = resolveColor(args,i+1);
          if(col != null)
            colIDBack = col;
        }
        else if(args[i].indexOf("-colMatchBack") > -1)
        {
          Color col = resolveColor(args,i+1);
          if(col != null)
            colMatchBack = col;
        }
        else if(args[i].indexOf("-colMatch") > -1)
        {
          Color col = resolveColor(args,i+1);
          if(col != null)
            colMatch = col;
        }
        else if(args[i].indexOf("-colID") > -1)
        {
          Color col = resolveColor(args,i+1);
          if(col != null)
            colID = col;
        }
        else if(args[i].indexOf("-minID") > -1)
          minID = Integer.parseInt(args[i+1]);
        else if(args[i].indexOf("-noBox") > -1)
          prettyBox = false;
        else if(args[i].indexOf("-font") > -1)
          gsc.setFontSizeForCollection(Integer.parseInt(args[i+1]));
        else if(args[i].indexOf("-landscape") > -1)
          landscape = true;
        else if(args[i].indexOf("-margin") > -1)
        {
          lmargin = Double.parseDouble(args[i+1]);
          rmargin = Double.parseDouble(args[i+2]);
          tmargin = Double.parseDouble(args[i+3]);
          bmargin = Double.parseDouble(args[i+4]);
        }
        else if(args[i].indexOf("-onePage") > -1)
          onePage = true;
        else if(args[i].indexOf("-antialias") > -1)
          antialias = true;
      }

      for(int i=0;i<args.length;i++)
      {
        if(args[i].indexOf("-color") > -1)
        {
          i++;
          if(args[i].startsWith("taylor"))      
            gsc.setColorScheme(SequenceProperties.taylorColor);
          else if(args[i].startsWith("residue"))
            gsc.setColorScheme(SequenceProperties.residueColor);
          else if(args[i].startsWith("rasmol"))
            gsc.setColorScheme(SequenceProperties.rasmolColor);
          else if(args[i].startsWith("acid"))
            gsc.setColorScheme(SequenceProperties.acidColor);
          else if(args[i].startsWith("polar"))
            gsc.setColorScheme(SequenceProperties.polarColor);
          else if(args[i].startsWith("hydro"))
            gsc.setColorScheme(SequenceProperties.hydrophobicColor);
          else if(args[i].startsWith("aromatic"))
            gsc.setColorScheme(SequenceProperties.aromaticColor);
          else if(args[i].startsWith("surface"))
            gsc.setColorScheme(SequenceProperties.surfaceColor);
          else if(args[i].startsWith("charge"))
            gsc.setColorScheme(SequenceProperties.chargeColor);
          else if(args[i].startsWith("size"))
            gsc.setColorScheme(SequenceProperties.sizeColor);
          else if(args[i].startsWith("base"))
            gsc.setColorScheme(SequenceProperties.baseColor);
        }
        else if(args[i].indexOf("-calc") > -1)
        {
          Consensus conseq = new Consensus(mat,
                    gsc.getSequenceCollection(),
                    plu,cas,ident);

          int fontSize = gsc.getFontSize();
          gsc.addSequence(conseq.getConsensusSequence(),true,5,fontSize);

          Dimension dpane = gsc.getPanelSize();
          gsc.setPreferredSize(dpane);
          gsc.setNamePanelWidth(gsc.getNameWidth());
        }
        else if(args[i].indexOf("-list") > -1)
          System.out.println("AVAILABLE DATABASES:\n"+
                             mat.getKeyNamesString());
        else if(args[i].indexOf("-id") > -1)
        {
          IDTableJFrame idtab = new IDTableJFrame(gsc.getSequenceCollection()); 
          idtab.printTable();
        }
        else if(args[i].indexOf("-noshow") > -1)
          show = false;
        else if(args[i].indexOf("-print") > -1)
          print = true;
        else if(args[i].indexOf("-nres")  > -1)
          nresiduesPerLine = Integer.parseInt(args[i+1]);
        else if(args[i].indexOf("-pretty")  > -1)          
        {
          PrettyPlotJFrame pretty = new PrettyPlotJFrame(minID,
                  match,colID,colMatch,
                  colIDBack,colMatchBack,prettyBox);
          gsc.setPrettyPlot(true,pretty);
          gsc.setDrawBoxes(false);
          gsc.setDrawColor(false);
        }  
        else if(args[i].indexOf("-preview")  > -1)
        {
          PrintAlignmentImage pai = new PrintAlignmentImage(gsc);
          pai.printPreview();
          show = true;
        }
        else if(args[i].indexOf("-type")  > -1)
        {
          if( args[i+1].equalsIgnoreCase("png") ||
              args[i+1].equalsIgnoreCase("jpeg") )
            type = args[i+1];
          else
            System.out.println("UNKOWN PRINT FORMAT: "+args[i+1]+
                               " reverting to default format "+type);
        }
        else if(args[i].indexOf("-prefix")  > -1)
          prefix = args[i+1];
      }

      if(print)
      {
        if(onePage)
        {
          PrintAlignmentImage pai = new PrintAlignmentImage(gsc);
          if(antialias)
            pai.setAntiAlias(true);
          pai.print(nresiduesPerLine,type,prefix,                               
                    lmargin,rmargin,tmargin,bmargin);
        }
        else
        {
          PrintAlignmentImage pai = new PrintAlignmentImage(gsc);
          if(antialias)
            pai.setAntiAlias(true);
          pai.print(nresiduesPerLine,type,prefix,landscape,
                    lmargin,rmargin,tmargin,bmargin);
        }
      }
      if(!show)
        System.exit(0);
    }
    else
    {
      ajFrame = new AlignJFrame(true);
    }
    ajFrame.setVisible(true);
  }


}