X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=15f1a1f86d8a6dfb77fe4af25a6e9421cf4ec5d1;hb=577f505f54fe343e89f581461e780ea8308c20ec;hp=fcb5a57a4849009c96b240c5f8ce0ffc9b584276;hpb=bfdb9a55949b38a89878959278a8b8ed82a55e49;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index fcb5a57..15f1a1f 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -8,6 +8,11 @@ import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
 
+import com.sun.image.codec.jpeg.*;
+import java.io.*;
+import java.awt.image.*;
+
+
 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
 {
 
@@ -15,11 +20,12 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   OverviewPanel overviewPanel;
   SeqPanel   seqPanel;
   IdPanel    idPanel;
+  SecondaryStructurePanel ssPanel;
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
   ScorePanel scorePanel;
 
-  public AlignmentPanel(AlignFrame af, AlignViewport av)
+  public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
     alignFrame = af;
     this.av         = av;
@@ -27,7 +33,9 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     idPanel         = new IdPanel   (av, this);
     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);
@@ -40,13 +48,54 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     addComponentListener(new ComponentAdapter()
    {
-       public void componentResized(ComponentEvent evt)
+     public void componentResized(ComponentEvent evt)
      {
           RefreshPanels();
      }
    });
+
+
+  // hscroll.setFocusable(false);
+  // vscroll.setFocusable(false);
+   setFocusable(true);
+
+   addKeyListener(new KeyAdapter()
+   {
+     public void keyPressed(KeyEvent evt)
+     {
+       switch(evt.getKeyCode())
+       {
+         case  27: // escape key
+           av.setSelectionGroup(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 );
@@ -75,19 +124,33 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   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)
   {
-      scalePanelHolder.setVisible(!wrap);
-      scorePanelHolder.setVisible(!wrap);
+    scorePanelHolder.setVisible(!wrap);
+    scalePanelHolder.setVisible(!wrap);
+    secondaryPanelHolder.setVisible(!wrap);
+
+    hscroll.setVisible(!wrap);
+
+    idSpaceFillerPanel.setVisible(!wrap);
+    idSpaceFillerPanel1.setVisible(!wrap);
+
+    RefreshPanels();
 
-      hscroll.setVisible(!wrap);
-      idSpaceFillerPanel.setVisible(!wrap);
-      idSpaceFillerPanel1.setVisible(!wrap);
   }
 
 
@@ -98,8 +161,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     if(av.getConservationSelected())
     {
 
-      Alignment al = (Alignment)av.getAlignment();
-      Conservation c = new Conservation("All",
+       Alignment al = (Alignment)av.getAlignment();
+       Conservation c = new Conservation("All",
                             ResidueProperties.propHash, 3, al.getSequences(), 0,
                             al.getWidth() );
 
@@ -110,175 +173,89 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
        av.setGlobalColourScheme( ccs );
 
     }
-    seqPanel.seqCanvas.paintFlag = true;
-    repaint();
-  }
-  /*
-    seqCanvas.paintFlag = true;
-    if (av.getSelection().size() == 0)
-    {
-      seqCanvas.globalColorScheme = cs;
-      for (int i = 0; i < av.alignment.getGroups().size();i++)
-      {
-        SequenceGroup sg = (SequenceGroup)av.alignment.getGroups().elementAt(i);
-        sg.cs = cs;
-        if(!showConservation
-            && !(sg.cs instanceof Blosum62ColourScheme)
-            && sg.cs instanceof ConservationColourScheme)
-         {
-           // remove ConservationColouring from existing Conservation group
-           ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-           sg.cs = ccs.cs;
-         }
-         else if(showConservation && !(sg.cs instanceof ConservationColourScheme))
-         {
-           // add ConservationColouring to new group
-           Conservation c = sg.getConservation();
-           Alignment al = (Alignment) av.getAlignment();
-           c = new Conservation("All", al.cons,
-                                ResidueProperties.propHash, 3, sg.sequences, 0,
-                                al.getWidth() );
-           c.calculate();
-           c.verdict(false, 100);
-           sg.setConservation(c);
-           sg.cs = new ConservationColourScheme(sg);
-         }
-      }
-    }
-    else
-    {
-      SequenceGroup sg = av.alignment.findGroup((Sequence)av.sel.sequenceAt(0));
-
-      if( isNewSelection(sg) )
-      {
-        sg = av.getAlignment().addGroup();
-        for (int i=0; i < av.getSelection().size(); i++)
-        {
-          av.alignment.removeFromGroup(av.alignment.findGroup( (Sequence) av.
-              sel.sequenceAt(i)),
-                                       (Sequence) av.sel.sequenceAt(i));
-          av.alignment.addToGroup(sg, (Sequence) av.sel.sequenceAt(i));
-        }
-      }
 
-
-      sg.cs = cs;
-
-      // Selection is made, we only want to change the conservationColour for selected group
-      if(  showConservation
-           && !(sg.cs instanceof ConservationColourScheme)
-           && !(sg.cs instanceof Blosum62ColourScheme))
-      {
-        Conservation c = sg.getConservation();
-        Alignment al = (Alignment) av.getAlignment();
-
-        c = new Conservation("All", al.cons,
-                             ResidueProperties.propHash, 3, sg.sequences, 0,
-                             al.getWidth() );
-        c.calculate();
-        c.verdict(false, 100);
-        sg.setConservation(c);
-        sg.cs = new ConservationColourScheme(sg);
-    }
-    else  if( !showConservation && sg.cs instanceof ConservationColourScheme)
-    {
-      ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-      sg.cs = ccs.cs;
-    }
-   }
-   repaint();
+    RefreshPanels();
   }
 
-  boolean isNewSelection(SequenceGroup sg)
+  public void RefreshPanels()
   {
-    if(sg==null)
-      return true;
-
-    if(sg.getSize()!=av.getSelection().size())
-      return true;
-
-    for(int i=0; i<sg.getSize(); i++)
-     if( !av.getSelection().contains( sg.getSequenceAt(i) ))
-       return true;
-
-    return false;
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+          {
+            public void run()
+            {
+
+              requestFocus();
+              invalidate();
+              idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());
+              hscrollFillerPanel.setPreferredSize(new Dimension(idPanel.idCanvas.
+                  getPreferredSize().width, 12));
+              idSpaceFillerPanel1.setPreferredSize(new Dimension(500,
+                  av.charHeight / 2 + 12));
+              scalePanelHolder.setPreferredSize(new Dimension(500,
+                  av.charHeight / 2 + 12));
+              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;
+  int vextent = 0;
 
 
-  public ColourSchemeI getColourScheme()
+  // return value is true if the scroll is valid
+  public boolean scrollUp(boolean up)
   {
-    if(av.getSelection().size()>0)
-       return av.alignment.findGroup((Sequence)av.sel.sequenceAt(0)).cs;
+    if(up)
+    {
+      if(vscroll.getValue()<1)
+        return false;
+      vscroll.setValue(vscroll.getValue() - 1);
+    }
     else
-      return seqCanvas.globalColorScheme;
-  }
-*/
-
-/*  public void setColourScheme(jalview.schemes.ColourSchemeI cs, boolean conservation)
-  {
-    seqPanel.setColourScheme(cs, conservation);
-
-    av.setGlobalColourScheme(cs);
+    {
+     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
+       return false;
+      vscroll.setValue(vscroll.getValue() + 1);
+    }
 
-    if(overviewPanel!=null)
-      overviewPanel.updateOverviewImage();
+    return true;
   }
 
-   void updateResidueView()
-   {
-     if (viewport.getSelection().size() == 0)
-      {
-        for (int i = 0; i < viewport.alignment.getGroups().size(); i++)
-        {
-          SequenceGroup sg = (SequenceGroup) viewport.alignment.getGroups().elementAt(i);
-          sg.setDisplayBoxes( viewBoxesMenuItem.isSelected() );
-          sg.setDisplayText( viewTextMenuItem.isSelected() );
-          sg.setColourText( colourTextMenuItem.isSelected() );
-        }
-      }
-      else
-      {
-        SequenceGroup sg = viewport.alignment.findGroup( (Sequence) viewport.sel.sequenceAt(0));
-        if (alignPanel.seqPanel.isNewSelection(sg))
-        {
-          sg = viewport.getAlignment().addGroup();
-          for (int i = 0; i < viewport.getSelection().size(); i++)
-          {
-            viewport.alignment.removeFromGroup(viewport.alignment.findGroup( (
-                Sequence) viewport.sel.sequenceAt(i)),
-                                               (Sequence) viewport.sel.sequenceAt(
-                i));
-            viewport.alignment.addToGroup(sg,
-                                          (Sequence) viewport.sel.sequenceAt(i));
-          }
-        }
-
-        sg.setDisplayBoxes(viewBoxesMenuItem.isSelected());
-        sg.setDisplayText(viewTextMenuItem.isSelected());
-        sg.setColourText(colourTextMenuItem.isSelected());
-      }
-     alignPanel.RefreshPanels();
-   }*/
-
-
-
-  public void RefreshPanels()
+  public boolean scrollRight(boolean right)
   {
-    invalidate();
-    seqPanel.seqCanvas.paintFlag = true;
-    idPanel.idCanvas.paintFlag = true;
-    idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
-    setScrollValues(av.getStartRes(), av.getStartSeq());
-    av.getConsensus(true);
-    validate();
-    repaint();
-    if(overviewPanel!=null)
-      overviewPanel.updateOverviewImage();
+    if(right)
+   {
+     if(hscroll.getValue()<1)
+       return false;
+     hscroll.setValue(hscroll.getValue() - 1);
+   }
+   else
+   {
+    if(hextent+hscroll.getValue() >= av.getAlignment().getWidth())
+      return false;
+     hscroll.setValue(hscroll.getValue() + 1);
+   }
 
-  }
+   return true;
+ }
 
-  int hextent = 0;
-  int vextent = 0;
 
   public void setScrollValues(int x, int y)
   {
@@ -299,6 +276,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     hscroll.setValues(x,hextent,0,av.getAlignment().getWidth());
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
+
+
     repaint();
 
   }
@@ -316,29 +295,44 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     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();
 
-    seqPanel.seqCanvas.paintFlag=true;
     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();
+    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() );
@@ -370,7 +364,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     ////////////////
     //draw Scale
     pg.translate(idWidth,0);
-    scalePanel.scaleCanvas.drawScale(pg, startRes, endRes, pwidth-idWidth);
+    scalePanel.drawScale(pg, startRes, endRes, pwidth-idWidth);
 
     pg.translate(-idWidth, 30);
     ////////////////
@@ -379,7 +373,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     Color currentTextColor=null;
     for(int i=startSeq; i<endSeq; i++)
     {
-      if (av.getSelection().contains(av.getAlignment().getSequenceAt(i)))
+      if (av.alignment.findGroup(av.getAlignment().getSequenceAt(i))==null)
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
@@ -410,6 +404,106 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     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.setFileView(new jalview.io.JalviewFileView());
+      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 ");
+    }
+  }
+
 }