X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=f1874b161a5a82aa55297c1739c6d456e1950625;hb=00f6edbbdddf16f77142e98e375363675be807fe;hp=d4788f2d4f8829936b7c3ec642bc84c626c669e2;hpb=2f75e4ae854e11477d7dac4591d7104de4dec7d9;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index d4788f2..f1874b1 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -7,10 +7,11 @@ import jalview.datamodel.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
-
-import com.sun.image.codec.jpeg.*;
 import java.io.*;
 import java.awt.image.*;
+import org.jibble.epsgraphics.*;
+import javax.imageio.*;
+
 
 
 public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListener, Printable
@@ -20,10 +21,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   OverviewPanel overviewPanel;
   SeqPanel   seqPanel;
   IdPanel    idPanel;
-  SecondaryStructurePanel ssPanel;
+  IdwidthAdjuster idwidthAdjuster;
   public AlignFrame alignFrame;
   ScalePanel scalePanel;
-  ScorePanel scorePanel;
+  AnnotationPanel annotationPanel;
+  AnnotationLabels alabels;
+
+  // this value is set false when selection area being dragged
+  boolean fastPaint = true;
 
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
@@ -31,34 +36,32 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     this.av         = av;
     seqPanel        = new SeqPanel  (av, this);
     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();
+    idwidthAdjuster = new IdwidthAdjuster(this);
+    idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+
+    annotationPanel = new AnnotationPanel(this);
+    alabels = new AnnotationLabels(this);
+
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+    annotationScroller.setViewportView(annotationPanel);
+    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+
+    fontChanged();
+
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-    setScrollValues(0,0);
+
+    setScrollValues(0, 0);
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
 
-    addComponentListener(new ComponentAdapter()
-   {
-     public void componentResized(ComponentEvent evt)
-     {
-          RefreshPanels();
-     }
-   });
-
-
-   hscroll.setFocusable(false);
-   vscroll.setFocusable(false);
    setFocusable(true);
-
    addKeyListener(new KeyAdapter()
    {
      public void keyPressed(KeyEvent evt)
@@ -66,19 +69,23 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
        switch(evt.getKeyCode())
        {
          case  27: // escape key
-           av.setRubberbandGroup(null);
-           RefreshPanels();
+           av.setSelectionGroup(null);
+           repaint();
            break;
          case KeyEvent.VK_X:
+           if(evt.isControlDown())
            alignFrame.cut_actionPerformed(null);
            break;
          case KeyEvent.VK_C:
+         if(evt.isControlDown())
            alignFrame.copy_actionPerformed(null);
            break;
          case KeyEvent.VK_V:
+          if(evt.isControlDown())
            alignFrame.paste(true);
            break;
          case KeyEvent.VK_A:
+         if(evt.isControlDown())
            alignFrame.selectAllSequenceMenuItem_actionPerformed(null);
            break;
         case KeyEvent.VK_DOWN:
@@ -88,6 +95,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
           alignFrame.moveSelectedSequences(true);
           break;
         case KeyEvent.VK_F:
+         if(evt.isControlDown())
           alignFrame.findMenuItem_actionPerformed(null);
           break;
        }
@@ -95,6 +103,66 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    });
   }
 
+  public void fontChanged()
+  {
+    // set idCanvas bufferedImage to null
+    // to prevent drawing old image
+    idPanel.idCanvas.gg = null;
+    annotationPanel.adjustPanelHeight();
+    Dimension d = calculateIdWidth();
+    d.setSize(d.width + 4, d.height);
+    idPanel.idCanvas.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(d);
+    repaint();
+  }
+
+
+  Dimension calculateIdWidth()
+  {
+    Graphics g = this.getGraphics();
+    if(g==null)
+    {
+      javax.swing.JFrame f = new javax.swing.JFrame();
+      f.addNotify();
+      g = f.getGraphics();
+    }
+
+    FontMetrics fm = g.getFontMetrics(av.font);
+    AlignmentI al = av.getAlignment();
+
+       int i   = 0;
+       int idWidth = 0;
+       String id;
+       while (i < al.getHeight() && al.getSequenceAt(i) != null)
+       {
+         SequenceI s   = al.getSequenceAt(i);
+         if(av.getShowFullId())
+           id   = s.getDisplayId();
+         else
+           id = s.getName();
+
+         if (fm.stringWidth(id) > idWidth)
+           idWidth = fm.stringWidth(id);
+         i++;
+       }
+
+       // Also check annotation label widths
+       i=0;
+       if(al.getAlignmentAnnotation()!=null)
+       {
+         fm = g.getFontMetrics(alabels.getFont());
+         while (i < al.getAlignmentAnnotation().length)
+         {
+           String label = al.getAlignmentAnnotation()[i].label;
+           if (fm.stringWidth(label) > idWidth)
+             idWidth = fm.stringWidth(label);
+           i++;
+         }
+       }
+
+       return new Dimension(idWidth, 12);
+  }
+
 
  public void highlightSearchResults(int [] results)
  {
@@ -122,34 +190,25 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
  }
 
 
-  public void setGraphPanelVisible(boolean b)
+  public void setAnnotationVisible(boolean b)
   {
-    idSpaceFillerPanel.setVisible(b);
-    scorePanelHolder.setVisible(b);
-
-    RefreshPanels();
-    // bit annoying to call this twice, can you do better?
-    RefreshPanels();
+    annotationSpaceFillerHolder.setVisible(b);
+    annotationScroller.setVisible(b);
   }
 
-  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);
+    idwidthAdjuster.setVisible(!wrap);
 
-    idSpaceFillerPanel.setVisible(!wrap);
+    av.setShowAnnotation(!wrap);
+    annotationScroller.setVisible(!wrap);
+    annotationSpaceFillerHolder.setVisible(!wrap);
     idSpaceFillerPanel1.setVisible(!wrap);
 
-    RefreshPanels();
+    repaint();
 
   }
 
@@ -167,49 +226,74 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
                             al.getWidth() );
 
        c.calculate();
-       c.verdict(false, 100);
+       c.verdict(false, av.ConsPercGaps);
        ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
 
        av.setGlobalColourScheme( ccs );
 
     }
 
-    RefreshPanels();
+    repaint();
   }
 
-  public void RefreshPanels()
-  {
-    requestFocus();
-    invalidate();
-    idPanelHolder.setPreferredSize( idPanel.idCanvas.getPreferredSize() );
 
-    if(av.getWrapAlignment())
-    {
-      int max = av.alignment.getWidth()/ (seqPanel.seqCanvas.getWidth()/av.charWidth)+1;
+  int hextent = 0;
+  int vextent = 0;
 
-      int h  = (av.alignment.getHeight() + 2)*av.charHeight;
-      vextent = seqPanel.seqCanvas.getHeight()/h;
-      vscroll.setValues(0,vextent,0,max);
+  // return value is true if the scroll is valid
+  public boolean scrollUp(boolean up)
+  {
+    if(up)
+    {
+      if(vscroll.getValue()<1)
+        return false;
+      fastPaint  = false;
+      vscroll.setValue(vscroll.getValue() - 1);
     }
     else
+    {
+     if(vextent+vscroll.getValue() >= av.getAlignment().getHeight())
+       return false;
+      fastPaint  = false;
+      vscroll.setValue(vscroll.getValue() + 1);
+    }
+    fastPaint = true;
+    return true;
+  }
 
-    setScrollValues(av.getStartRes(), av.getStartSeq());
-    av.getConsensus(true);
-    if(overviewPanel!=null)
-      overviewPanel.updateOverviewImage();
-
-    validate();
-    repaint();
+  public boolean scrollRight(boolean right)
+  {
 
+    if (right)
+    {
+      if (hscroll.getValue() < 1)
+        return false;
+      fastPaint = false;
+      hscroll.setValue(hscroll.getValue() - 1);
+    }
+    else
+    {
+      if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
+        return false;
+      fastPaint = false;
+      hscroll.setValue(hscroll.getValue() + 1);
+    }
+    fastPaint = true;
+    return true;
   }
 
-  int hextent = 0;
-  int vextent = 0;
 
   public void setScrollValues(int x, int y)
   {
-    hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
-    vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
+    av.setEndRes(x + seqPanel.seqCanvas.getWidth()/av.getCharWidth()-1);
+
+    hextent = seqPanel.seqCanvas.getWidth()/av.charWidth;
+    vextent = seqPanel.seqCanvas.getHeight()/av.charHeight;
+
+    if(hextent > av.alignment.getWidth())
+      hextent = av.alignment.getWidth();
+    if(vextent > av.alignment.getHeight())
+      vextent = av.alignment.getHeight();
 
     if(hextent+x  >  av.getAlignment().getWidth())
       x =  av.getAlignment().getWidth()- hextent;
@@ -227,13 +311,14 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     vscroll.setValues(y,vextent,0,av.getAlignment().getHeight() );
 
 
-    repaint();
 
   }
 
 
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
+    int oldX = av.getStartRes();
+    int oldY = av.getStartSeq();
 
     if (evt.getSource() == hscroll)
     {
@@ -247,7 +332,9 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       int offy = vscroll.getValue();
       if (av.getWrapAlignment())
       {
-        av.setStartRes( vscroll.getValue() * av.getChunkWidth());
+        int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+        av.setStartRes( vscroll.getValue() * rowSize );
+        av.setEndRes( (vscroll.getValue()+1) * rowSize );
       }
       else
       {
@@ -256,11 +343,49 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       }
     }
 
-
     if(overviewPanel!=null)
       overviewPanel.setBoxPosition();
 
-    repaint();
+    if(av.getWrapAlignment() || !fastPaint)
+      repaint();
+    else
+    {
+      idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
+      seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
+                                   av.getStartSeq() - oldY);
+
+      scalePanel.repaint();
+      if (av.getShowAnnotation())
+        annotationPanel.fastPaint(av.getStartRes() - oldX);
+    }
+
+  }
+
+
+  public void paintComponent(Graphics g)
+  {
+    invalidate();
+    Dimension d = idPanel.idCanvas.getPreferredSize();
+    idPanelHolder.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+    validate();
+
+    if (av.getWrapAlignment())
+    {
+      int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+      vscroll.setMaximum(max);
+      vscroll.setUnitIncrement(1);
+      vscroll.setVisibleAmount(1);
+    }
+    else
+    {
+      if (overviewPanel != null)
+        overviewPanel.updateOverviewImage();
+      setScrollValues(av.getStartRes(), av.getStartSeq());
+    }
+
+
+
   }
 
   public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
@@ -279,7 +404,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
   {
 
-    int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
+    int idWidth = calculateIdWidth().width + 4;
 
 
     pg.setColor(Color.white);
@@ -313,7 +438,7 @@ 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);
     ////////////////
@@ -322,7 +447,7 @@ 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.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
@@ -340,16 +465,27 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
       pg.setColor(currentTextColor);
 
-      String string = av.getAlignment().getSequenceAt(i).getDisplayId();
+      String string = av.getAlignment().getSequenceAt(i).getName();
+      if(av.getShowFullId())
+        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);
 
+
+    if(av.getShowAnnotation())
+      {
+        pg.translate(-idWidth,(endSeq-startSeq)*av.charHeight);
+        alabels.drawComponent((Graphics2D)pg);
+        pg.translate(idWidth,0);
+        annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes+1);
+      }
+
     return Printable.PAGE_EXISTS;
   }
 
@@ -357,7 +493,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
   public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException
   {
 
-    int idWidth = (int)idPanel.idCanvas.getLabelWidth().getWidth();
+    int idWidth = calculateIdWidth().width+4;
 
     if( seqPanel.seqCanvas.getWidth() < pwidth-idWidth)
       pwidth = seqPanel.seqCanvas.getWidth() + idWidth;
@@ -382,18 +518,23 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
     ////////////////
     // Draw the ids
-    pg.setClip(0,0,pwidth, noChunksOnPage*chunkHeight);
+//    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++ )
+
+    int rowSize =  av.getEndRes() - av.getStartRes();
+    for(int ypos=2*av.charHeight, row=av.getEndRes()-rowSize;
+              ypos <= pheight && row<av.alignment.getWidth();
+              ypos += av.chunkHeight, row+=rowSize )
     {
       for (int i = 0; i < endy; i++)
       {
         SequenceI s = da.getSequenceAt(i);
-        pg.drawString(s.getDisplayId(), 0,
+        String string = s.getName();
+        if (av.getShowFullId())
+          string = s.getDisplayId();
+
+        pg.drawString(string, 0,
                       AlignmentUtil.getPixelHeight(0, i, av.charHeight) + ypos +
                       av.charHeight - (av.charHeight / 5));
       }
@@ -408,47 +549,102 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
   }
 
-  public void makeJPG(int width, int height)
+
+  public void makeEPS()
   {
+    int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
+    int width = seqPanel.getWidth() + idPanel.getWidth();
+
+    if (!av.getWrapAlignment())
+    {
+      height = (av.alignment.getHeight()+1) * av.charHeight + 30;
+      width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
+    }
+    if(av.getShowAnnotation())
+   {
+     height += annotationPanel.getPreferredSize().height;
+   }
+
     try
     {
+      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+          "LAST_DIRECTORY"), new String[]{"eps"}, "Encapsulated Postscript");
+      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setDialogTitle("Create EPS file from alignment");
+      chooser.setToolTipText("Save");
+
+      int value = chooser.showSaveDialog(this);
+      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        return;
 
-      BufferedImage bi = new BufferedImage(width, height,
-                                           BufferedImage.TYPE_INT_RGB);
-      Graphics pg = bi.getGraphics();
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
+      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
+      EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width, height);
 
-      try
-      {
         if (av.getWrapAlignment())
           printWrappedAlignment(pg, width, height, 0);
         else
           printUnwrapped(pg, width, height, 0);
+
+
+        pg.flush();
+        pg.close();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  public void makePNG()
+  {
+      int height = (av.alignment.getWidth() / av.getChunkWidth() +1) * av.chunkHeight;
+      int width = seqPanel.getWidth() + idPanel.getWidth();
+
+      if (!av.getWrapAlignment())
+      {
+        height = (av.alignment.getHeight()+1) * av.charHeight + 30;
+        width = idPanel.getWidth() + av.alignment.getWidth() * av.charWidth;
       }
-      catch (Exception ex)
-      {}
 
-      javax.swing.JFileChooser chooser = new javax.swing.JFileChooser(jalview.bin.Cache.getProperty(
-          "LAST_DIRECTORY"));
-      chooser.setDialogTitle("Create JPG image from alignment");
+      if(av.getShowAnnotation())
+      {
+        height += annotationPanel.getPreferredSize().height;
+      }
+
+
+
+    try
+    {
+      jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(jalview.bin.Cache.getProperty(
+          "LAST_DIRECTORY"), new String[]{"png"}, "Portable network graphics");
+      chooser.setFileView(new jalview.io.JalviewFileView());
+      chooser.setDialogTitle("Create EPS file from alignment");
       chooser.setToolTipText("Save");
 
       int value = chooser.showSaveDialog(this);
-      if (value == javax.swing.JFileChooser.APPROVE_OPTION)
-      {
+      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        return;
 
-        FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
-        JPEGImageEncoder jie = JPEGCodec.createJPEGEncoder(out);
-        JPEGEncodeParam param = JPEGCodec.getDefaultJPEGEncodeParam(bi);
-        param.setQuality(1.0f, true);
+      jalview.bin.Cache.setProperty("LAST_DIRECTORY",chooser.getSelectedFile().getPath());
+      FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
 
-        jie.encode(bi, param);
-        out.close();
-      }
+      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+      Graphics2D png = (Graphics2D)bi.getGraphics();
+
+      png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,RenderingHints.VALUE_ANTIALIAS_ON);
+
+        if (av.getWrapAlignment())
+          printWrappedAlignment(png, width, height, 0);
+        else
+          printUnwrapped(png, width, height, 0);
 
+        ImageIO.write(bi, "png", out);
+        out.close();
     }
-    catch (IOException ex)
+    catch (Exception ex)
     {
-      System.out.println("ex Writing image ");
+      ex.printStackTrace();
     }
   }
 
@@ -456,3 +652,4 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
 
 
+