X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=bd43a978c259eb94fd712394363c9082aa76d947;hb=4ebc6d5b362bc093c39312aa1a69836e3dd6ae84;hp=fe03a31b731e6aad6285f3dc0eecbe0de4390a59;hpb=a35ccec335158616a10026952e0cefad8083fe62;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fe03a31..bd43a97 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,71 +1,86 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * 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 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.
+ *
+ * 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
+ */
 package jalview.gui;
 
+import java.util.*;
+
 import java.awt.*;
+
 import jalview.analysis.*;
-import jalview.analysis.NJTree;
+import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
-import java.util.*;
-import jalview.bin.Cache;
 
 public class AlignViewport
 {
   int startRes;
   int endRes;
-
   int startSeq;
   int endSeq;
-
   boolean showFullId = false;
-  boolean showText=true;
-  boolean showColourText=false;
-  boolean showBoxes=true;
-  boolean wrapAlignment=false;
+  boolean showText = true;
+  boolean showColourText = false;
+  boolean showBoxes = true;
+  boolean wrapAlignment = false;
   boolean renderGaps = true;
   boolean showSequenceFeatures = false;
   boolean showAnnotation = true;
   boolean showConservation = true;
   boolean showQuality = true;
   boolean showIdentity = true;
-
   boolean colourAppliesToAllGroups = true;
   ColourSchemeI globalColourScheme = null;
   boolean conservationColourSelected = false;
   boolean abovePIDThreshold = false;
-
   SequenceGroup selectionGroup = new SequenceGroup();
-
-
-  int             charHeight;
-  int             charWidth;
-  int             chunkWidth;
-  int             chunkHeight;
-
-  Font            font = new Font("SansSerif",Font.PLAIN,10);
-  AlignmentI      alignment;
-
+  int charHeight;
+  int charWidth;
+  int chunkWidth;
+  int chunkHeight;
+  Font font = new Font("SansSerif", Font.PLAIN, 10);
+  AlignmentI alignment;
   ColumnSelection colSel = new ColumnSelection();
-
   int threshold;
   int increment;
-
   NJTree currentTree = null;
-
   boolean scaleAboveWrapped = false;
-  boolean scaleLeftWrapped  = true;
+  boolean scaleLeftWrapped = true;
   boolean scaleRightWrapped = true;
+  public Vector vconsensus;
+  AlignmentAnnotation consensus;
+  AlignmentAnnotation conservation;
+  AlignmentAnnotation quality;
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
+  // JBPNote Prolly only need this in the applet version.
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.
+      PropertyChangeSupport(this);
 
   public AlignViewport(AlignmentI al)
   {
     setAlignment(al);
     this.startRes = 0;
-    this.endRes = al.getWidth()-1;
+    this.endRes = al.getWidth() - 1;
     this.startSeq = 0;
-    this.endSeq = al.getHeight()-1;
+    this.endSeq = al.getHeight() - 1;
 
     updateFromPreferences();
-
   }
 
   public void updateFromPreferences()
@@ -76,20 +91,30 @@ public class AlignViewport
     showQuality = Preferences.showQuality;
     showIdentity = Preferences.showIdentity;
     showFullId = Preferences.showFullId;
+
     String fontName = Preferences.fontName;
     String fontStyle = Preferences.fontStyle;
     String fontSize = Cache.getProperty("FONT_SIZE");
-    if (fontName != null && fontStyle != null && fontSize != null)
+
+    if ( (fontName != null) && (fontStyle != null) && (fontSize != null))
     {
       int style = 0;
-      if(fontStyle.equals("bold"))
+
+      if (fontStyle.equals("bold"))
+      {
         style = 1;
-      else if(fontStyle.equals("italic"))
+      }
+      else if (fontStyle.equals("italic"))
+      {
         style = 2;
+      }
+
       setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
     }
     else
+    {
       setFont(font);
+    }
 
     alignment.setGapCharacter(Preferences.gapSymbol);
 
@@ -97,49 +122,55 @@ public class AlignViewport
     // as Blosum and Clustal require this to be done
     updateConservation();
     updateConsensus();
-    if(Preferences.defaultColour!=null)
+
+    if (Preferences.defaultColour != null)
     {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment, Preferences.defaultColour);
-      if(globalColourScheme instanceof UserColourScheme)
+      globalColourScheme = ColourSchemeProperty.getColour(alignment,
+          Preferences.defaultColour);
+
+      if (globalColourScheme instanceof UserColourScheme)
       {
         globalColourScheme = UserDefinedColours.loadDefaultColours();
       }
-      if(globalColourScheme!=null)
-        globalColourScheme.setConsensus( vconsensus );
-   }
 
- }
-
- public void showSequenceFeatures(boolean b)
- {
-   showSequenceFeatures = b;
- }
-
-  public Vector vconsensus;
-  AlignmentAnnotation consensus;
-  AlignmentAnnotation conservation;
-  AlignmentAnnotation quality;
+      if (globalColourScheme != null)
+      {
+        globalColourScheme.setConsensus(vconsensus);
+      }
+    }
+  }
 
-  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+  public void showSequenceFeatures(boolean b)
+  {
+    showSequenceFeatures = b;
+  }
 
   public void updateConservation()
   {
     Conservation cons = new jalview.analysis.Conservation("All",
         jalview.schemes.ResidueProperties.propHash, 3,
-        alignment.getSequences(), 0,
-        alignment.getWidth()-1);
+        alignment.getSequences(), 0, alignment.getWidth() - 1);
     cons.calculate();
     cons.verdict(false, ConsPercGaps);
     cons.findQuality();
+
     int alWidth = alignment.getWidth();
-    Annotation [] annotations = new Annotation[alWidth];
-    Annotation [] qannotations = new Annotation[alWidth];
+    Annotation[] annotations = new Annotation[alWidth];
+    Annotation[] qannotations = new Annotation[alWidth];
     String sequence = cons.getConsSequence().getSequence();
-    float minR,minG,minB, maxR,maxG,maxB;
+    float minR;
+    float minG;
+    float minB;
+    float maxR;
+    float maxG;
+    float maxB;
     minR = 0.3f;
     minG = 0.0f;
     minB = 0f;
-    maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring both Conservation and Quality
+    maxR = 1.0f - minR;
+    maxG = 0.9f - minG;
+    maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
+
     float min = 0f;
     float max = 11f;
     float qmin = cons.qualityRange[0].floatValue();
@@ -148,108 +179,140 @@ public class AlignViewport
     for (int i = 0; i < alWidth; i++)
     {
       float value = 0;
+
       try
+      {
+        value = Integer.parseInt(sequence.charAt(i) + "");
+      }
+      catch (Exception ex)
+      {
+        if (sequence.charAt(i) == '*')
         {
-          value = Integer.parseInt(sequence.charAt(i) + "");
+          value = 11;
         }
-      catch (Exception ex)
+
+        if (sequence.charAt(i) == '+')
         {
-          if (sequence.charAt(i) == '*') value = 11;
-          if (sequence.charAt(i) == '+') value = 10;
+          value = 10;
         }
-      float vprop = value-min;
-      vprop/=max;
-      annotations[i] = new Annotation(sequence.charAt(i) + "",
-                                      "", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+      }
+
+      float vprop = value - min;
+      vprop /= max;
+      annotations[i] = new Annotation(sequence.charAt(i) + "", "", ' ',
+                                      value,
+                                      new Color(minR + (maxR * vprop),
+                                                minG + (maxG * vprop),
+                                                minB + (maxB * vprop)));
+
       // Quality calc
-      value = ((Double) cons.quality.get(i)).floatValue();
+      value = ( (Double) cons.quality.get(i)).floatValue();
       vprop = value - qmin;
-      vprop/=qmax;
-      qannotations[i] = new Annotation(" ",
-                                      String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));
+      vprop /= qmax;
+      qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',
+                                       value,
+                                       new Color(minR + (maxR * vprop),
+                                                 minG + (maxG * vprop),
+                                                 minB + (maxB * vprop)));
     }
 
-    if(conservation==null)
+    if (conservation == null)
     {
       conservation = new AlignmentAnnotation("Conservation",
-                                             "Conservation of total alignment less than "+ConsPercGaps+"% gaps",
-                                             annotations,
-                                             0f, // cons.qualityRange[0].floatValue(),
+                                             "Conservation of total alignment less than " +
+                                             ConsPercGaps + "% gaps",
+                                             annotations, 0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
                                              1);
-      if(showConservation)
-      alignment.addAnnotation(conservation);
+
+      if (showConservation)
+      {
+        alignment.addAnnotation(conservation);
+      }
+
       quality = new AlignmentAnnotation("Quality",
                                         "Alignment Quality based on Blosum62 scores",
                                         qannotations,
                                         cons.qualityRange[0].floatValue(),
-                                        cons.qualityRange[1].floatValue(),
-                                        1);
-      if(showQuality)
+                                        cons.qualityRange[1].floatValue(), 1);
+
+      if (showQuality)
+      {
         alignment.addAnnotation(quality);
+      }
     }
-    else {
+    else
+    {
       conservation.annotations = annotations;
       quality.annotations = qannotations;
       quality.graphMax = cons.qualityRange[1].floatValue();
     }
-
-
   }
 
   public void updateConsensus()
   {
-    Annotation [] annotations = new Annotation[alignment.getWidth()];
+    Annotation[] annotations = new Annotation[alignment.getWidth()];
 
     // this routine prevents vconsensus becoming a new object each time
     // consenus is calculated. Important for speed of Blosum62
     // and PID colouring of alignment
-    if(vconsensus == null)
-        vconsensus = alignment.getAAFrequency();
+    if (vconsensus == null)
+    {
+      vconsensus = alignment.getAAFrequency();
+    }
     else
     {
-        Vector temp = alignment.getAAFrequency();
-        vconsensus.clear();
-        Enumeration e = temp.elements();
-        while(e.hasMoreElements())
-        {
-          vconsensus.add(e.nextElement());
-        }
+      Vector temp = alignment.getAAFrequency();
+      vconsensus.clear();
+
+      Enumeration e = temp.elements();
+
+      while (e.hasMoreElements())
+      {
+        vconsensus.add(e.nextElement());
+      }
     }
+
     Hashtable hash = null;
-    for (int i = 0; i<alignment.getWidth(); i++)
+
+    for (int i = 0; i < alignment.getWidth(); i++)
     {
-        hash = (Hashtable) vconsensus.elementAt(i);
-        float value = Float.parseFloat(hash.get("maxCount").toString());
-        value /= Float.parseFloat(hash.get("size").toString());
-
-        value *= 100;
-        String maxRes = hash.get("maxResidue")+" ";
-        String mouseOver = hash.get("maxResidue")+" ";
-        if(maxRes.length()>2)
-        {
-          mouseOver = "["+maxRes+"] ";
-          maxRes = "+ ";
-        }
+      hash = (Hashtable) vconsensus.elementAt(i);
+
+      float value = Float.parseFloat(hash.get("maxCount").toString());
+      value /= Float.parseFloat(hash.get("size").toString());
 
-        mouseOver += (int)value+"%";
-        annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+      value *= 100;
 
+      String maxRes = hash.get("maxResidue") + " ";
+      String mouseOver = hash.get("maxResidue") + " ";
+
+      if (maxRes.length() > 2)
+      {
+        mouseOver = "[" + maxRes + "] ";
+        maxRes = "+ ";
+      }
+
+      mouseOver += ( (int) value + "%");
+      annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
     }
 
-     if(consensus==null)
-     {
-       consensus = new AlignmentAnnotation("Consensus",
-                                           "PID", annotations, 0f, 100f, 1);
-       if(showIdentity)
-         alignment.addAnnotation(consensus);
-     }
-     else
-       consensus.annotations = annotations;
+    if (consensus == null)
+    {
+      consensus = new AlignmentAnnotation("Consensus", "PID",
+                                          annotations, 0f, 100f, 1);
 
+      if (showIdentity)
+      {
+        alignment.addAnnotation(consensus);
+      }
+    }
+    else
+    {
+      consensus.annotations = annotations;
+    }
   }
 
-
   public SequenceGroup getSelectionGroup()
   {
     return selectionGroup;
@@ -260,42 +323,44 @@ public class AlignViewport
     selectionGroup = sg;
   }
 
+  public boolean getConservationSelected()
+  {
+    return conservationColourSelected;
+  }
 
- public boolean getConservationSelected()
- {
-   return conservationColourSelected;
- }
-
- public void setConservationSelected(boolean b)
- {
-   conservationColourSelected = b;
- }
+  public void setConservationSelected(boolean b)
+  {
+    conservationColourSelected = b;
+  }
 
- public boolean getAbovePIDThreshold()
- {
-   return abovePIDThreshold;
- }
+  public boolean getAbovePIDThreshold()
+  {
+    return abovePIDThreshold;
+  }
 
- public void setAbovePIDThreshold(boolean b)
- {
-   abovePIDThreshold = b;
- }
+  public void setAbovePIDThreshold(boolean b)
+  {
+    abovePIDThreshold = b;
+  }
 
-  public int getStartRes() {
+  public int getStartRes()
+  {
     return startRes;
   }
 
-  public int getEndRes() {
+  public int getEndRes()
+  {
     return endRes;
   }
 
-  public int getStartSeq() {
+  public int getStartSeq()
+  {
     return startSeq;
   }
 
   public void setGlobalColourScheme(ColourSchemeI cs)
   {
-     globalColourScheme = cs;
+    globalColourScheme = cs;
   }
 
   public ColourSchemeI getGlobalColourScheme()
@@ -303,91 +368,134 @@ public class AlignViewport
     return globalColourScheme;
   }
 
-
-  public void setStartRes(int res) {
+  public void setStartRes(int res)
+  {
     this.startRes = res;
   }
-  public void setStartSeq(int seq) {
+
+  public void setStartSeq(int seq)
+  {
     this.startSeq = seq;
   }
-  public void setEndRes(int res) {
-    if (res > alignment.getWidth()-1) {
+
+  public void setEndRes(int res)
+  {
+    if (res > (alignment.getWidth() - 1))
+    {
       // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
-       res = alignment.getWidth()-1;
+      res = alignment.getWidth() - 1;
     }
-    if (res < 0) {
+
+    if (res < 0)
+    {
       res = 0;
     }
+
     this.endRes = res;
   }
-  public void setEndSeq(int seq) {
-    if (seq > alignment.getHeight()) {
+
+  public void setEndSeq(int seq)
+  {
+    if (seq > alignment.getHeight())
+    {
       seq = alignment.getHeight();
     }
-    if (seq < 0) {
+
+    if (seq < 0)
+    {
       seq = 0;
     }
+
     this.endSeq = seq;
   }
-  public int getEndSeq() {
+
+  public int getEndSeq()
+  {
     return endSeq;
   }
 
-  public void setFont(Font f) {
+  public void setFont(Font f)
+  {
     font = f;
+
     javax.swing.JFrame temp = new javax.swing.JFrame();
     temp.addNotify();
+
     java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);
     setCharHeight(fm.getHeight());
     setCharWidth(fm.charWidth('M'));
   }
 
-  public Font getFont() {
+  public Font getFont()
+  {
     return font;
   }
-  public void setCharWidth(int w) {
+
+  public void setCharWidth(int w)
+  {
     this.charWidth = w;
   }
-  public int getCharWidth() {
+
+  public int getCharWidth()
+  {
     return charWidth;
   }
-  public void setCharHeight(int h) {
+
+  public void setCharHeight(int h)
+  {
     this.charHeight = h;
   }
-  public int getCharHeight() {
+
+  public int getCharHeight()
+  {
     return charHeight;
   }
-  public void setChunkWidth(int w) {
+
+  public void setChunkWidth(int w)
+  {
     this.chunkWidth = w;
   }
-  public int getChunkWidth() {
+
+  public int getChunkWidth()
+  {
     return chunkWidth;
   }
-  public void setChunkHeight(int h) {
+
+  public void setChunkHeight(int h)
+  {
     this.chunkHeight = h;
   }
-  public int getChunkHeight() {
+
+  public int getChunkHeight()
+  {
     return chunkHeight;
   }
-  public AlignmentI getAlignment() {
+
+  public AlignmentI getAlignment()
+  {
     return alignment;
   }
-  public void setAlignment(AlignmentI align) {
+
+  public void setAlignment(AlignmentI align)
+  {
     this.alignment = align;
   }
 
-  public void setWrapAlignment(boolean state) {
+  public void setWrapAlignment(boolean state)
+  {
     wrapAlignment = state;
   }
-  public void setShowText(boolean state) {
+
+  public void setShowText(boolean state)
+  {
     showText = state;
   }
 
-  public void setRenderGaps(boolean state){
+  public void setRenderGaps(boolean state)
+  {
     renderGaps = state;
   }
 
-
   public boolean getColourText()
   {
     return showColourText;
@@ -398,79 +506,117 @@ public class AlignViewport
     showColourText = state;
   }
 
-  public void setShowBoxes(boolean state) {
+  public void setShowBoxes(boolean state)
+  {
     showBoxes = state;
   }
 
-  public boolean getWrapAlignment() {
-      return wrapAlignment;
+  public boolean getWrapAlignment()
+  {
+    return wrapAlignment;
   }
-  public boolean getShowText() {
+
+  public boolean getShowText()
+  {
     return showText;
   }
-  public boolean getShowBoxes() {
+
+  public boolean getShowBoxes()
+  {
     return showBoxes;
   }
 
-  public char getGapCharacter() {
+  public char getGapCharacter()
+  {
     return getAlignment().getGapCharacter();
   }
-  public void setGapCharacter(char gap) {
-    if (getAlignment() != null) {
+
+  public void setGapCharacter(char gap)
+  {
+    if (getAlignment() != null)
+    {
       getAlignment().setGapCharacter(gap);
     }
   }
-  public void setThreshold(int thresh) {
+
+  public void setThreshold(int thresh)
+  {
     threshold = thresh;
   }
-  public int getThreshold() {
+
+  public int getThreshold()
+  {
     return threshold;
   }
-  public void setIncrement(int inc) {
+
+  public void setIncrement(int inc)
+  {
     increment = inc;
   }
-  public int getIncrement() {
+
+  public int getIncrement()
+  {
     return increment;
   }
-  public int getIndex(int y) {
-    int y1     = 0;
+
+  public int getIndex(int y)
+  {
+    int y1 = 0;
     int starty = getStartSeq();
-    int endy   = getEndSeq();
+    int endy = getEndSeq();
 
-    for (int i = starty; i <= endy; i++) {
-      if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {
+    for (int i = starty; i <= endy; i++)
+    {
+      if ( (i < alignment.getHeight()) &&
+          (alignment.getSequenceAt(i) != null))
+      {
         int y2 = y1 + getCharHeight();
 
-        if (y>=y1 && y <=y2) {
+        if ( (y >= y1) && (y <= y2))
+        {
           return i;
         }
-        y1  = y2;
-      } else {
+
+        y1 = y2;
+      }
+      else
+      {
         return -1;
       }
     }
+
     return -1;
   }
 
-  public ColumnSelection getColumnSelection() {
+  public ColumnSelection getColumnSelection()
+  {
     return colSel;
   }
 
-  public void resetSeqLimits(int height) {
-    setEndSeq(height/getCharHeight());
+  public void resetSeqLimits(int height)
+  {
+    setEndSeq(height / getCharHeight());
   }
-  public void setCurrentTree(NJTree tree) {
-      currentTree = tree;
+
+  public void setCurrentTree(NJTree tree)
+  {
+    currentTree = tree;
   }
-  public NJTree getCurrentTree() {
+
+  public NJTree getCurrentTree()
+  {
     return currentTree;
   }
 
   public void setColourAppliesToAllGroups(boolean b)
-  {   colourAppliesToAllGroups = b; }
+  {
+    colourAppliesToAllGroups = b;
+  }
 
   public boolean getColourAppliesToAllGroups()
-  {return colourAppliesToAllGroups; }
+  {
+    return colourAppliesToAllGroups;
+  }
 
   public boolean getShowFullId()
   {
@@ -483,38 +629,59 @@ public class AlignViewport
   }
 
   public boolean getShowAnnotation()
-  {   return showAnnotation;  }
+  {
+    return showAnnotation;
+  }
 
   public void setShowAnnotation(boolean b)
-  {    showAnnotation = b;  }
+  {
+    showAnnotation = b;
+  }
 
   public boolean getScaleAboveWrapped()
-  { return scaleAboveWrapped;}
+  {
+    return scaleAboveWrapped;
+  }
 
   public boolean getScaleLeftWrapped()
-  { return scaleLeftWrapped; }
+  {
+    return scaleLeftWrapped;
+  }
 
   public boolean getScaleRightWrapped()
-  { return scaleRightWrapped; }
+  {
+    return scaleRightWrapped;
+  }
 
   public void setScaleAboveWrapped(boolean b)
-  { scaleAboveWrapped = b; }
+  {
+    scaleAboveWrapped = b;
+  }
 
   public void setScaleLeftWrapped(boolean b)
-  { scaleLeftWrapped = b; }
+  {
+    scaleLeftWrapped = b;
+  }
 
   public void setScaleRightWrapped(boolean b)
-  { scaleRightWrapped = b; }
-  // JBPNote Prolly only need this in the applet version.
-  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
-  public void addPropertyChangeListener(java.beans.PropertyChangeListener listener) {
+  {
+    scaleRightWrapped = b;
+  }
+
+  public void addPropertyChangeListener(
+      java.beans.PropertyChangeListener listener)
+  {
     changeSupport.addPropertyChangeListener(listener);
   }
 
-  public void removePropertyChangeListener(java.beans.PropertyChangeListener listener) {
+  public void removePropertyChangeListener(
+      java.beans.PropertyChangeListener listener)
+  {
     changeSupport.removePropertyChangeListener(listener);
   }
-  public void firePropertyChange(String prop, Object oldvalue, Object newvalue) {
+
+  public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+  {
     changeSupport.firePropertyChange(prop, oldvalue, newvalue);
   }
 }