X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=75729c330775e2b93ab5067126233e926b726e18;hb=8004878db16757b62ee2c35738506bc4509428cf;hp=296bb80cd7224af3030611f3d705c60ab23fe64c;hpb=e61e2b53cc88a6dd4dd5abe857b19172f253ba11;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 296bb80..75729c3 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)
   {
@@ -31,35 +36,43 @@ 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);
 
-    javax.swing.JFrame f = new javax.swing.JFrame();
-    f.addNotify();
-    FontMetrics fm = f.getGraphics().getFontMetrics(av.font);
-    AlignmentI al = av.getAlignment();
+    annotationPanel = new AnnotationPanel(this);
+    alabels = new AnnotationLabels(this);
 
-    int i   = 0;
-    int idWidth = 0;
-    while (i < al.getHeight() && al.getSequenceAt(i) != null)
-    {
-      SequenceI s   = al.getSequenceAt(i);
-      String str   = s.getDisplayId();
-      if (fm.stringWidth(str) > idWidth)
-        idWidth = fm.stringWidth(str);
-      i++;
-    }
-    hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12));
+    annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());
+    annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());
+    annotationScroller.setViewportView(annotationPanel);
+    annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+
+    Dimension d = calculateIdWidth();
+    d.setSize( d.width+4, d.height);
+    idPanel.idCanvas.setPreferredSize( d );
+    hscrollFillerPanel.setPreferredSize( d );
 
     scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
-    scorePanelHolder.add(scorePanel, BorderLayout.CENTER);
     seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
-    setScrollValues(0,0);
+
+
+    if(seqPanel.seqCanvas.getWidth()==0)
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+     {
+       public void run()
+       {
+         setScrollValues(0,0);
+         Dimension d = calculateIdWidth();
+         d.setSize( d.width+4, d.height);
+         idPanel.idCanvas.setPreferredSize( d );
+         RefreshPanels();
+       }
+    });
+
 
     hscroll.addAdjustmentListener(this);
     vscroll.addAdjustmentListener(this);
@@ -72,11 +85,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
      }
    });
 
-
-  // hscroll.setFocusable(false);
-  // vscroll.setFocusable(false);
    setFocusable(true);
-
    addKeyListener(new KeyAdapter()
    {
      public void keyPressed(KeyEvent evt)
@@ -88,15 +97,19 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
            RefreshPanels();
            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:
@@ -106,6 +119,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
           alignFrame.moveSelectedSequences(true);
           break;
         case KeyEvent.VK_F:
+         if(evt.isControlDown())
           alignFrame.findMenuItem_actionPerformed(null);
           break;
        }
@@ -113,6 +127,38 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
    });
   }
 
+  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++;
+       }
+
+       return new Dimension(idWidth, 12);
+  }
+
 
  public void highlightSearchResults(int [] results)
  {
@@ -140,31 +186,30 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
  }
 
 
-  public void setGraphPanelVisible(boolean b)
+  public void setAnnotationVisible(boolean b)
   {
-    idSpaceFillerPanel.setVisible(b);
-    scorePanelHolder.setVisible(b);
+    annotationSpaceFillerHolder.setVisible(b);
+    annotationScroller.setVisible(b);
+    javax.swing.SwingUtilities.invokeLater(new Runnable()
+     {
+       public void run()
+       {
+         RefreshPanels();
+       }
+    });
 
-    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);
+    idwidthAdjuster.setVisible(!wrap);
 
-    idSpaceFillerPanel.setVisible(!wrap);
+    av.setShowAnnotation(!wrap);
+    annotationScroller.setVisible(!wrap);
+    annotationSpaceFillerHolder.setVisible(!wrap);
     idSpaceFillerPanel1.setVisible(!wrap);
 
     RefreshPanels();
@@ -195,40 +240,36 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     RefreshPanels();
   }
 
+
   public void RefreshPanels()
   {
-              requestFocus();
-              invalidate();
-              idPanelHolder.setPreferredSize(idPanel.idCanvas.getPreferredSize());
-              if(idPanel.idCanvas.getPreferredSize()!=null)
-                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();
+    requestFocus();
+    invalidate();
+
+    Dimension d = idPanel.idCanvas.getPreferredSize();
+    idPanelHolder.setPreferredSize(d);
+    hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+
+    if (av.getWrapAlignment())
+    {
+      int max = av.alignment.getWidth() /
+          (seqPanel.seqCanvas.getWidth() / av.charWidth) + 1;
+      vscroll.setValues(0, 1, 0, max);
+    }
+    else
+    {
+      if (overviewPanel != null)
+        overviewPanel.updateOverviewImage();
+      setScrollValues(av.getStartRes(), av.getStartSeq());
+    }
+
+    validate();
+    repaint();
   }
+
   int hextent = 0;
   int vextent = 0;
 
-
   // return value is true if the scroll is valid
   public boolean scrollUp(boolean up)
   {
@@ -236,41 +277,51 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     {
       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;
   }
 
   public boolean scrollRight(boolean right)
   {
-    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;
- }
+    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;
+  }
 
 
   public void setScrollValues(int x, int y)
   {
-    hextent = seqPanel.seqCanvas.getWidth()/av.getCharWidth();
-    vextent = seqPanel.seqCanvas.getHeight()/av.getCharHeight();
+    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;
@@ -287,14 +338,13 @@ 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)
   {
+    int oldX = av.getStartRes();
+    int oldY = av.getStartSeq();
 
     if (evt.getSource() == hscroll)
     {
@@ -321,7 +371,18 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     if(overviewPanel!=null)
       overviewPanel.setBoxPosition();
 
-    repaint();
+    if(av.getWrapAlignment() || !fastPaint)
+      repaint();
+    else
+    {
+      seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX,
+                                   av.getStartSeq() - oldY);
+      idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY);
+      scalePanel.repaint();
+      if (av.getShowAnnotation())
+        annotationPanel.fastPaint(av.getStartRes() - oldX);
+    }
+
   }
 
   public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException
@@ -340,7 +401,7 @@ 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);
@@ -383,7 +444,7 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
     Color currentTextColor=null;
     for(int i=startSeq; i<endSeq; i++)
     {
-      if (av.alignment.findGroup(av.getAlignment().getSequenceAt(i))==null)
+      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(av.getAlignment().getSequenceAt(i)))
       {
         currentColor = Color.gray;
         currentTextColor = Color.black;
@@ -401,16 +462,27 @@ 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;
   }
 
@@ -418,7 +490,7 @@ 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;
@@ -454,7 +526,11 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
       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));
       }
@@ -469,48 +545,102 @@ 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");
 
-      BufferedImage bi = new BufferedImage(width, height,
-                                           BufferedImage.TYPE_INT_RGB);
-      Graphics pg = bi.getGraphics();
+      int value = chooser.showSaveDialog(this);
+      if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+        return;
+
+      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"));
+      if(av.getShowAnnotation())
+      {
+        height += annotationPanel.getPreferredSize().height;
+      }
+
+
+System.out.println(width +" "+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 JPG image from alignment");
+      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());
+
+      BufferedImage bi = new BufferedImage(width, height, BufferedImage.TYPE_INT_RGB);
+      Graphics png = bi.getGraphics();
 
-        jie.encode(bi, param);
-        out.close();
-      }
 
+        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();
     }
   }
 
@@ -518,3 +648,4 @@ public class AlignmentPanel extends GAlignmentPanel implements AdjustmentListene
 
 
 
+