X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=d4788f2d4f8829936b7c3ec642bc84c626c669e2;hb=2f75e4ae854e11477d7dac4591d7104de4dec7d9;hp=cf3e3df661db8376e5320cc2eab2edc8b9273004;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index cf3e3df..d4788f2 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,32 +1,43 @@
 package jalview.gui;
 
 import jalview.jbgui.GAlignmentPanel;
+import jalview.schemes.*;
+import jalview.analysis.*;
+import jalview.datamodel.*;
 import java.awt.*;
-import javax.swing.*;
 import java.awt.event.*;
+import java.awt.print.*;
 
-public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener
+import com.sun.image.codec.jpeg.*;
+import java.io.*;
+import java.awt.image.*;
+
+
+public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
 {
 
   AlignViewport     av;
-  public SeqPanel   seqPanel;
-  public IdPanel    idPanel;
+  OverviewPanel overviewPanel;
+  SeqPanel   seqPanel;
+  IdPanel    idPanel;
+  SecondaryStructurePanel ssPanel;
   public AlignFrame alignFrame;
-  public ScalePanel scalePanel;
-  public ScorePanel scorePanel;
+  ScalePanel scalePanel;
+  ScorePanel scorePanel;
 
-  public boolean    groupEdit = false;
-
-  public AlignmentPanel(AlignFrame af, AlignViewport av)
+  public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     alignFrame = af;
     this.av         = av;
     seqPanel        = new SeqPanel  (av, this);
     idPanel         = new IdPanel   (av, this);
-    scalePanel = new ScalePanel(av);
+    scalePanel = new ScalePanel(av, this);
     scorePanel = new ScorePanel(av);
+    ssPanel = new SecondaryStructurePanel(av);
 
+    secondaryPanelHolder.add(ssPanel, BorderLayout.CENTER);
     idPanelHolder.add(idPanel, BorderLayout.CENTER);
+    idPanel.addNotify();
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
     scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
@@ -34,56 +45,162 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
-    selectAll(false);
 
     addComponentListener(new ComponentAdapter()
    {
-       public void componentResized(ComponentEvent evt)
-     {      RefreshPanels();    }
+     public void componentResized(ComponentEvent evt)
+     {
+          RefreshPanels();
+     }
    });
 
-  }
 
-  public int countSelected()
-  {
-    return av.getSelection().size();
-  }
+   hscroll.setFocusable(false);
+   vscroll.setFocusable(false);
+   setFocusable(true);
 
-  public void selectAll(boolean flag) {
-    int i = 0;
-    if (flag) {
-      while (i < seqPanel.align.getHeight()) {
-        if (! av.getSelection().contains(av.getAlignment().getSequenceAt(i))) {
-          av.getSelection().addElement(av.getAlignment().getSequenceAt(i));
-        }
-        i++;
-      }
-    } else {
-      av.getSelection().clear();
-    }
+   addKeyListener(new KeyAdapter()
+   {
+     public void keyPressed(KeyEvent evt)
+     {
+       switch(evt.getKeyCode())
+       {
+         case  27: // escape key
+           av.setRubberbandGroup(null);
+           RefreshPanels();
+           break;
+         case KeyEvent.VK_X:
+           alignFrame.cut_actionPerformed(null);
+           break;
+         case KeyEvent.VK_C:
+           alignFrame.copy_actionPerformed(null);
+           break;
+         case KeyEvent.VK_V:
+           alignFrame.paste(true);
+           break;
+         case KeyEvent.VK_A:
+           alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
+           break;
+        case KeyEvent.VK_DOWN:
+          alignFrame.moveSelectedSequences(false);
+          break;
+        case KeyEvent.VK_UP:
+          alignFrame.moveSelectedSequences(true);
+          break;
+        case KeyEvent.VK_F:
+          alignFrame.findMenuItem_actionPerformed(null);
+          break;
+       }
+     }
+   });
   }
 
 
+ public void highlightSearchResults(int [] results)
+ {
+   seqPanel.seqCanvas.highlightSearchResults( results );
+
+   // do we need to scroll the panel?
+   if(results!=null && (av.getStartSeq()>results[0]
+                        || av.getEndSeq()<results[0]
+                        || av.getStartRes()>results[1]
+                        || av.getEndRes()<results[2]))
+       setScrollValues(results[1], results[0]);
+
+
+ }
+
+
+ public OverviewPanel getOverviewPanel()
+ {
+   return overviewPanel;
+ }
+
+ public void setOverviewPanel(OverviewPanel op)
+ {
+   overviewPanel = op;
+ }
+
 
   public void setGraphPanelVisible(boolean b)
   {
-    scorePanelHolder.setVisible(b);
     idSpaceFillerPanel.setVisible(b);
+    scorePanelHolder.setVisible(b);
+
+    RefreshPanels();
+    // bit annoying to call this twice, can you do better?
+    RefreshPanels();
+  }
+
+  public void setSecondaryStructureVisible(boolean b)
+  {
+    secondaryPanelHolder.setVisible(b);
     RefreshPanels();
   }
 
+  public void setWrapAlignment(boolean wrap)
+  {
+    scorePanelHolder.setVisible(!wrap);
+    scalePanelHolder.setVisible(!wrap);
+    secondaryPanelHolder.setVisible(!wrap);
+
+    hscroll.setVisible(!wrap);
+
+    idSpaceFillerPanel.setVisible(!wrap);
+    idSpaceFillerPanel1.setVisible(!wrap);
+
+    RefreshPanels();
+
+  }
 
 
+  public void setColourScheme()
+  {
+    ColourSchemeI cs = av.getGlobalColourScheme();
+
+    if(av.getConservationSelected())
+    {
+
+       Alignment al = (Alignment)av.getAlignment();
+       Conservation c = new Conservation("All",
+                            ResidueProperties.propHash, 3, al.getSequences(), 0,
+                            al.getWidth() );
+
+       c.calculate();
+       c.verdict(false, 100);
+       ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
+
+       av.setGlobalColourScheme( ccs );
+
+    }
+
+    RefreshPanels();
+  }
+
   public void RefreshPanels()
   {
+    requestFocus();
     invalidate();
     idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
-    validate();
-    idPanel.idCanvas.paintFlag = true;
-    seqPanel.seqCanvas.paintFlag = true;
+
+    if(av.getWrapAlignment())
+    {
+      int max = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;
+
+      int h  = (av.alignment.getHeight() + 2)*av.charHeight;
+      vextent = seqPanel.seqCanvas.getHeight()/h;
+      vscroll.setValues(0,vextent,0,max);
+    }
+    else
+
     setScrollValues(av.getStartRes(), av.getStartSeq());
     av.getConsensus(true);
+    if(overviewPanel!=null)
+      overviewPanel.updateOverviewImage();
+
+    validate();
     repaint();
+
   }
 
   int hextent = 0;
@@ -91,7 +208,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   public void setScrollValues(int x, int y)
   {
-    hextent = (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth());
+    hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
     vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
 
     if(hextent+x  >  av.getAlignment().getWidth())
@@ -109,28 +226,233 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
 
+
+    repaint();
+
   }
 
 
-  public void adjustmentValueChanged(AdjustmentEvent evt) {
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
 
     if (evt.getSource() == hscroll)
     {
       int x = hscroll.getValue();
       av.setStartRes(x);
-      av.setEndRes(x + (int)(seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1));
+      av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
     }
 
     if (evt.getSource() == vscroll)
     {
-        int offy = vscroll.getValue();
+      int offy = vscroll.getValue();
+      if (av.getWrapAlignment())
+      {
+        av.setStartRes( vscroll.getValue() * av.getChunkWidth());
+      }
+      else
+      {
         av.setStartSeq(offy);
-        av.setEndSeq(offy + seqPanel.seqCanvas.getHeight()/av.getCharHeight());
+        av.setEndSeq(offy + seqPanel.seqCanvas.getHeight() / av.getCharHeight());
+      }
     }
 
+
+    if(overviewPanel!=null)
+      overviewPanel.setBoxPosition();
+
     repaint();
   }
 
+  public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
+  {
+    pg.translate((int)pf.getImageableX(), (int)pf.getImageableY());
 
+    int pwidth = (int) pf.getImageableWidth();
+    int pheight = (int) pf.getImageableHeight();
+
+    if (av.getWrapAlignment())
+      return printWrappedAlignment(pg, pwidth,pheight, pi);
+    else
+      return printUnwrapped(pg,pwidth, pheight,pi);
+  }
+
+  public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
+  {
+
+    int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
+
+
+    pg.setColor(Color.white);
+    pg.fillRect(0,0,pwidth, pheight);
+    pg.setFont( av.getFont() );
+
+    ////////////////////////////////////
+    /// How many sequences and residues can we fit on a printable page?
+    int totalRes = (pwidth - idWidth)/av.getCharWidth();
+    int totalSeq = (int)((pheight - 30)/av.getCharHeight())-1;
+    int pagesWide = av.getAlignment().getWidth() / totalRes +1;
+    int pagesHigh = av.getAlignment().getHeight() / totalSeq +1;
+
+    if (pi >= pagesWide*pagesHigh)
+     return Printable.NO_SUCH_PAGE;
+
+    /////////////////////////////
+    /// Only print these sequences and residues on this page
+    int startRes, endRes, startSeq, endSeq;
+    startRes = (pi % pagesWide) * totalRes;
+    endRes = startRes + totalRes-1;
+    if(endRes>av.getAlignment().getWidth())
+      endRes = av.getAlignment().getWidth();
+
+     startSeq = (pi / pagesWide) * totalSeq;
+     endSeq = startSeq + totalSeq;
+     if(endSeq > av.getAlignment().getHeight())
+       endSeq = av.getAlignment().getHeight();
+
+
+    ////////////////
+    //draw Scale
+    pg.translate(idWidth,0);
+    scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);
+
+    pg.translate(-idWidth, 30);
+    ////////////////
+    // Draw the ids
+    Color currentColor=null;
+    Color currentTextColor=null;
+    for(int i=startSeq; i<endSeq; i++)
+    {
+      if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
+      {
+        currentColor = Color.gray;
+        currentTextColor = Color.black;
+      }
+      else
+      {
+        currentColor = av.getAlignment().getSequenceAt(i).getColor();
+        currentTextColor = Color.black;
+      }
+
+      pg.setColor(currentColor);
+      pg.fillRect(0,  jalview.analysis.AlignmentUtil.getPixelHeight(startSeq, i, av.getCharHeight()),
+                              idWidth,
+                              av.getCharHeight());
+
+      pg.setColor(currentTextColor);
+
+      String string = av.getAlignment().getSequenceAt(i).getDisplayId();
+      pg.drawString(string, 0,  jalview.analysis.AlignmentUtil.getPixelHeight
+                    (startSeq, i, av.getCharHeight()) + av.getCharHeight() - (av.getCharHeight() / 5));
+    }
+
+    // draw main sequence panel
+    pg.translate(idWidth,0);
+    pg.setClip(0,0,pwidth-idWidth, pheight);
+    seqPanel.seqCanvas.drawPanel(pg,startRes,endRes,startSeq,endSeq,startRes,startSeq,0);
+
+    return Printable.PAGE_EXISTS;
+  }
+
+
+  public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
+  {
+
+    int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
+
+    if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
+      pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
+
+
+    pg.setColor(Color.white);
+    pg.fillRect(0,0,pwidth, pheight);
+    pg.setFont( av.getFont() );
+
+    ////////////////////////////////////
+    /// How many sequences and residues can we fit on a printable page?
+    AlignmentI da = av.alignment;
+    int endy   = da.getHeight();
+    int chunkHeight =  (da.getHeight() + 2)*av.charHeight;
+    int chunkWidth  =   (pwidth-idWidth)/av.charWidth;
+
+    int noChunksOnPage = pheight / chunkHeight;
+    int totalChunks = da.getWidth() / chunkWidth;
+
+    if ( pi*noChunksOnPage > totalChunks )
+     return Printable.NO_SUCH_PAGE;
+
+    ////////////////
+    // Draw the ids
+    pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
+
+    int row = pi*noChunksOnPage;
+    pg.setColor(Color.black);
+    for(int ypos=2*av.charHeight;
+        ypos <= pheight && row*chunkWidth<da.getWidth();
+        ypos += chunkHeight, row++ )
+    {
+      for (int i = 0; i < endy; i++)
+      {
+        SequenceI s = da.getSequenceAt(i);
+        pg.drawString(s.getDisplayId(), 0,
+                      AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
+                      av.charHeight - (av.charHeight / 5));
+      }
+    }
+
+    // draw main sequence panel
+    pg.translate(idWidth,0);
+    seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth-idWidth, pheight, pi*noChunksOnPage*chunkWidth);
+
+
+    return Printable.PAGE_EXISTS;
+
+  }
+
+  public void makeJPG(int width, int height)
+  {
+    try
+    {
+
+      BufferedImage bi = new BufferedImage(width, height,
+                                           BufferedImage.TYPE_INT_RGB);
+      Graphics pg = bi.getGraphics();
+
+      try
+      {
+        if (av.getWrapAlignment())
+          printWrappedAlignment(pg, width, height, 0);
+        else
+          printUnwrapped(pg, width, height, 0);
+      }
+      catch (Exception ex)
+      {}
+
+      javax.swing.JFileChooser chooser = new javax.swing.JFileChooser(jalview.bin.Cache.getProperty(
+          "LAST_DIRECTORY"));
+      chooser.setDialogTitle("Create JPG image from alignment");
+      chooser.setToolTipText("Save");
+
+      int value = chooser.showSaveDialog(this);
+      if (value == javax.swing.JFileChooser.APPROVE_OPTION)
+      {
+
+        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+        JPEGImageEncoder jie = JPEGCodec.createJPEGEncoder(out);
+        JPEGEncodeParam param = JPEGCodec.getDefaultJPEGEncodeParam(bi);
+        param.setQuality(1.0f, true);
+
+        jie.encode(bi, param);
+        out.close();
+      }
+
+    }
+    catch (IOException ex)
+    {
+      System.out.println("ex Writing image ");
+    }
+  }
 
 }
+
+
+