X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=743d217fb10508d7b98de06e91473040b40a3156;hb=aa6643d51133a8541dcbe30191b344aa09907a5f;hp=06df9f4fb909640b9579ac89599246d70cbd1ab7;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 06df9f4..743d217 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,56 +1,65 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
+import jalview.viewmodel.OverviewDimensions;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
 
 public class OverviewPanel extends Panel implements Runnable,
         MouseMotionListener, MouseListener
 {
-  Image miniMe;
-
-  Image offscreen;
-
-  AlignViewport av;
+  private OverviewDimensions od;
 
-  AlignmentPanel ap;
+  private Image miniMe;
 
-  float scalew = 1f;
+  private Image offscreen;
 
-  float scaleh = 1f;
+  private AlignViewport av;
 
-  public int width, sequencesHeight;
+  private AlignmentPanel ap;
 
-  int graphHeight = 20;
+  private boolean resizing = false;
 
-  int boxX = -1, boxY = -1, boxWidth = -1, boxHeight = -1;
-
-  boolean resizing = false;
+  // This is set true if the user resizes whilst
+  // the overview is being calculated
+  private boolean resizeAgain = false;
 
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
-  SequenceRenderer sr;
+  private SequenceRenderer sr;
 
-  FeatureRenderer fr;
+  private FeatureRenderer fr;
 
-  Frame nullFrame;
+  private Frame nullFrame;
 
   public OverviewPanel(AlignmentPanel ap)
   {
@@ -65,46 +74,18 @@ public class OverviewPanel extends Panel implements Runnable,
     sr.renderGaps = false;
     sr.forOverview = true;
     fr = new FeatureRenderer(av);
-    fr.overview = true;
-
-    // scale the initial size of overviewpanel to shape of alignment
-    float initialScale = (float) av.alignment.getWidth()
-            / (float) av.alignment.getHeight();
 
-    if (av.hconsensus == null)
-    {
-      graphHeight = 0;
-    }
-
-    if (av.alignment.getWidth() > av.alignment.getHeight())
-    {
-      // wider
-      width = 400;
-      sequencesHeight = (int) (400f / initialScale);
-      if (sequencesHeight < 40)
-      {
-        sequencesHeight = 40;
-      }
-    }
-    else
-    {
-      // taller
-      width = (int) (400f * initialScale);
-      sequencesHeight = 300;
-      if (width < 120)
-      {
-        width = 120;
-      }
-    }
+    od = new OverviewDimensions(av);
 
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
+    setSize(new Dimension(od.getWidth(), od.getHeight()));
     addComponentListener(new ComponentAdapter()
     {
 
+      @Override
       public void componentResized(ComponentEvent evt)
       {
-        if (getSize().width != width
-                || getSize().height != sequencesHeight + graphHeight)
+        if ((getWidth() != od.getWidth())
+                || (getHeight() != (od.getHeight())))
         {
           updateOverviewImage();
         }
@@ -119,90 +100,57 @@ public class OverviewPanel extends Panel implements Runnable,
 
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
-    boxX = evt.getX();
-    boxY = evt.getY();
+    od.setBoxX(evt.getX());
+    od.setBoxY(evt.getY());
     checkValid();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
-    boxX = evt.getX();
-    boxY = evt.getY();
+    od.setBoxX(evt.getX());
+    od.setBoxY(evt.getY());
     checkValid();
   }
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
-    boxX = evt.getX();
-    boxY = evt.getY();
+    od.setBoxX(evt.getX());
+    od.setBoxY(evt.getY());
     checkValid();
   }
 
-  void checkValid()
+  /**
+   * Check box dimensions and scroll positions and correct if necessary
+   */
+  private void checkValid()
   {
-    if (boxY < 0)
-    {
-      boxY = 0;
-    }
-
-    if (boxY > (sequencesHeight - boxHeight))
-    {
-      boxY = sequencesHeight - boxHeight + 1;
-    }
-
-    if (boxX < 0)
-    {
-      boxX = 0;
-    }
-
-    if (boxX > (width - boxWidth))
-    {
-      if (av.hasHiddenColumns)
-      {
-        // Try smallest possible box
-        boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
-      }
-      boxX = width - boxWidth;
-    }
-
-    int col = (int) (boxX / scalew / av.getCharWidth());
-    int row = (int) (boxY / scaleh / av.getCharHeight());
-
-    if (av.hasHiddenColumns)
-    {
-      if (!av.getColumnSelection().isVisible(col))
-      {
-        return;
-      }
-
-      col = av.getColumnSelection().findColumnPosition(col);
-    }
-
-    if (av.hasHiddenRows)
-    {
-      row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
-              row);
-    }
-
-    ap.setScrollValues(col, row);
+    od.checkValid();
+    ap.setScrollValues(od.getScrollCol(), od.getScrollRow());
     ap.paintAlignment(false);
   }
 
@@ -217,159 +165,69 @@ public class OverviewPanel extends Panel implements Runnable,
       return;
     }
 
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
-      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
-      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+      fr.transferSettings(ap.seqPanel.seqCanvas.fr);
     }
 
     resizing = true;
 
-    if ((getSize().width > 0) && (getSize().height > 0))
+    if ((getWidth() > 0) && (getHeight() > 0))
     {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
+      od.setWidth(getWidth()); // width = getWidth();
+      od.setHeight(getHeight()); // sequencesHeight = getHeight() - graphHeight;
     }
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
+    setSize(new Dimension(od.getWidth(), od.getHeight()));
 
     Thread thread = new Thread(this);
     thread.start();
     repaint();
   }
 
-  // This is set true if the user resizes whilst
-  // the overview is being calculated
-  boolean resizeAgain = false;
-
+  @Override
   public void run()
   {
     miniMe = null;
-    int alwidth = av.alignment.getWidth();
-    int alheight = av.alignment.getHeight();
 
-    if (av.showSequenceFeatures)
+    if (av.isShowSequenceFeatures())
     {
       fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
     }
 
     if (getSize().width > 0 && getSize().height > 0)
     {
-      width = getSize().width;
-      sequencesHeight = getSize().height - graphHeight;
+      od.setWidth(getSize().width);
+      od.setHeight(getSize().height - od.getGraphHeight());
     }
 
-    setSize(new Dimension(width, sequencesHeight + graphHeight));
+    setSize(new Dimension(od.getWidth(), od.getHeight()));
 
-    int fullsizeWidth = alwidth * av.getCharWidth();
-    int fullsizeHeight = alheight * av.getCharHeight();
-
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    miniMe = nullFrame.createImage(width, sequencesHeight + graphHeight);
-    offscreen = nullFrame.createImage(width, sequencesHeight + graphHeight);
+    miniMe = nullFrame.createImage(od.getWidth(), od.getHeight());
+    offscreen = nullFrame.createImage(od.getWidth(), od.getHeight());
 
     Graphics mg = miniMe.getGraphics();
-    float sampleCol = (float) alwidth / (float) width;
-    float sampleRow = (float) alheight / (float) sequencesHeight;
-
-    int lastcol = 0, lastrow = 0;
-    int xstart = 0, ystart = 0;
-    Color color = Color.yellow;
-    int row, col, sameRow = 0, sameCol = 0;
-    jalview.datamodel.SequenceI seq;
-    boolean hiddenRow = false;
-    for (row = 0; row <= sequencesHeight; row++)
-    {
-      if ((int) (row * sampleRow) == lastrow)
-      {
-        sameRow++;
-        continue;
-      }
-
-      hiddenRow = false;
-      if (av.hasHiddenRows)
-      {
-        seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
-        if (seq == null)
-        {
-          int index = av.alignment.getHiddenSequences()
-                  .findIndexWithoutHiddenSeqs(lastrow);
-
-          seq = av.alignment.getSequenceAt(index);
-        }
-        else
-        {
-          hiddenRow = true;
-        }
-      }
-      else
-      {
-        seq = av.alignment.getSequenceAt(lastrow);
-      }
-
-      for (col = 0; col < width; col++)
-      {
-        if ((int) (col * sampleCol) == lastcol
-                && (int) (row * sampleRow) == lastrow)
-        {
-          sameCol++;
-          continue;
-        }
-
-        lastcol = (int) (col * sampleCol);
-
-        if (seq.getLength() > lastcol)
-        {
-          color = sr.getResidueBoxColour(seq, lastcol);
 
-          if (av.showSequenceFeatures)
-          {
-            color = fr.findFeatureColour(color, seq, lastcol);
-          }
-        }
-        else
-        {
-          color = Color.white; // White
-        }
-
-        if (hiddenRow
-                || (av.hasHiddenColumns && !av.getColumnSelection()
-                        .isVisible(lastcol)))
-        {
-          color = color.darker().darker();
-        }
+    od.updateScales();
 
-        mg.setColor(color);
-        if (sameCol == 1 && sameRow == 1)
-        {
-          mg.drawLine(xstart, ystart, xstart, ystart);
-        }
-        else
-        {
-          mg.fillRect(xstart, ystart, sameCol, sameRow);
-        }
+    int alwidth = av.getAlignment().getWidth();
+    int alheight = av.getAlignment().getHeight()
+            + av.getAlignment().getHiddenSequences().getSize();
+    float sampleCol = alwidth / (float) od.getWidth();
+    float sampleRow = alheight / (float) od.getSequencesHeight();
 
-        xstart = col;
-        sameCol = 1;
-      }
-      lastrow = (int) (row * sampleRow);
-      ystart = row;
-      sameRow = 1;
-    }
+    buildImage(sampleRow, sampleCol, mg);
 
-    if (av.conservation != null)
+    if (av.getAlignmentConservationAnnotation() != null)
     {
-      for (col = 0; col < width; col++)
+      for (int col = 0; col < od.getWidth() && !resizeAgain; col++)
       {
-        lastcol = (int) (col * sampleCol);
-        {
-          mg.translate(col, sequencesHeight);
-          ap.annotationPanel.drawGraph(mg, av.conservation,
-                  (int) (sampleCol) + 1, graphHeight,
-                  (int) (col * sampleCol), (int) (col * sampleCol) + 1);
-          mg.translate(-col, -sequencesHeight);
-        }
+        mg.translate(col, od.getSequencesHeight());
+        ap.annotationPanel.renderer.drawGraph(mg,
+                av.getAlignmentConservationAnnotation(),
+                av.getAlignmentConservationAnnotation().annotations,
+                (int) (sampleCol) + 1, od.getGraphHeight(),
+                (int) (col * sampleCol), (int) (col * sampleCol) + 1);
+        mg.translate(-col, -od.getSequencesHeight());
       }
     }
     System.gc();
@@ -385,60 +243,139 @@ public class OverviewPanel extends Panel implements Runnable,
     }
   }
 
-  public void setBoxPosition()
+  private void buildImage(float sampleRow, float sampleCol, Graphics mg)
   {
-    int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
-    int fullsizeHeight = (av.alignment.getHeight() + av.alignment
-            .getHiddenSequences().getSize())
-            * av.getCharHeight();
-
-    int startRes = av.getStartRes();
-    int endRes = av.getEndRes();
-
-    if (av.hasHiddenColumns)
-    {
-      startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
-      endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
-    }
+    int lastcol = 0;
+    int lastrow = 0;
+    int xstart = 0;
+    int ystart = 0;
+    Color color = Color.yellow;
+    int sameRow = 0;
+    int sameCol = 0;
 
-    int startSeq = av.startSeq;
-    int endSeq = av.endSeq;
+    jalview.datamodel.SequenceI seq = null;
+    final boolean hasHiddenRows = av.hasHiddenRows();
+    final boolean hasHiddenCols = av.hasHiddenColumns();
+    boolean hiddenRow = false;
 
-    if (av.hasHiddenRows)
+    for (int row = 0; row <= od.getSequencesHeight() && !resizeAgain; row++)
     {
-      startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(
-              startSeq);
+      if ((int) (row * sampleRow) == lastrow)
+      {
+        sameRow++;
+        continue;
+      }
+      else
+      {
+        // this should largely be a method in Alignment
+        hiddenRow = false;
+        if (hasHiddenRows)
+        {
+          seq = av.getAlignment().getHiddenSequences()
+                  .getHiddenSequence(lastrow);
+          if (seq == null)
+          {
+            int index = av.getAlignment().getHiddenSequences()
+                    .findIndexWithoutHiddenSeqs(lastrow);
 
-      endSeq = av.alignment.getHiddenSequences()
-              .adjustForHiddenSeqs(endSeq);
+            seq = av.getAlignment().getSequenceAt(index);
+          }
+          else
+          {
+            hiddenRow = true;
+          }
+        }
+        else
+        {
+          seq = av.getAlignment().getSequenceAt(lastrow);
+        }
+        // end of Alignment method
 
+        for (int col = 0; col < od.getWidth(); col++)
+        {
+          if ((int) (col * sampleCol) == lastcol
+                  && (int) (row * sampleRow) == lastrow)
+          {
+            sameCol++;
+          }
+          else
+          {
+            lastcol = (int) (col * sampleCol);
+
+            color = getColumnColourFromSequence(seq, hiddenRow,
+                    hasHiddenCols, lastcol);
+
+            mg.setColor(color);
+            if (sameCol == 1 && sameRow == 1)
+            {
+              mg.drawLine(xstart, ystart, xstart, ystart);
+            }
+            else
+            {
+              mg.fillRect(xstart, ystart, sameCol, sameRow);
+            }
+
+            xstart = col;
+            sameCol = 1;
+          }
+        }
+        lastrow = (int) (row * sampleRow);
+        ystart = row;
+        sameRow = 1;
+      }
     }
 
-    scalew = (float) width / (float) fullsizeWidth;
-    scaleh = (float) sequencesHeight / (float) fullsizeHeight;
-
-    boxX = (int) (startRes * av.getCharWidth() * scalew);
-    boxY = (int) (startSeq * av.getCharHeight() * scaleh);
+  }
 
-    if (av.hasHiddenColumns)
+  /*
+   * Find the colour of a sequence at a specified column position
+   */
+  private Color getColumnColourFromSequence(
+          jalview.datamodel.SequenceI seq, boolean hiddenRow,
+          boolean hasHiddenCols, int lastcol)
+  {
+    Color color;
+    if (seq.getLength() > lastcol)
     {
-      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+      color = sr.getResidueBoxColour(seq, lastcol);
+
+      if (av.isShowSequenceFeatures())
+      {
+        color = fr.findFeatureColour(color, seq, lastcol);
+      }
     }
     else
     {
-      boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
+      color = Color.white; // White
     }
 
-    boxHeight = (int) ((endSeq - startSeq) * av.getCharHeight() * scaleh);
+    if (hiddenRow
+            || (hasHiddenCols && !av.getColumnSelection()
+                    .isVisible(lastcol)))
+    {
+      color = color.darker().darker();
+    }
+    return color;
+  }
 
+  /**
+   * Update the overview panel box when the associated alignment panel is
+   * changed
+   * 
+   */
+  public void setBoxPosition()
+  {
+    od.setBoxPosition();
     repaint();
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     Graphics og = offscreen.getGraphics();
@@ -446,8 +383,10 @@ public class OverviewPanel extends Panel implements Runnable,
     {
       og.drawImage(miniMe, 0, 0, this);
       og.setColor(Color.red);
-      og.drawRect(boxX, boxY, boxWidth, boxHeight);
-      og.drawRect(boxX + 1, boxY + 1, boxWidth - 2, boxHeight - 2);
+      og.drawRect(od.getBoxX(), od.getBoxY(), od.getBoxWidth(),
+              od.getBoxHeight());
+      og.drawRect(od.getBoxX() + 1, od.getBoxY() + 1, od.getBoxWidth() - 2,
+              od.getBoxHeight() - 2);
       g.drawImage(offscreen, 0, 0, this);
     }
   }