X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=9f6448d513ceb2a995cff47383a2cbc2b265b609;hb=2ad64bdec4782e3fbfa3b5867a1aa7d1571629fa;hp=e7cae4434305e6beea837c9fc87f28067a0db551;hpb=9fff97021c2c637e426f6971d54dcf3fd4191985;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e7cae44..9f6448d 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -36,7 +36,10 @@ public class AlignViewport
   int startSeq;
   int endSeq;
 
-  boolean showFullId = true;
+
+  boolean cursorMode = false;
+
+  boolean showJVSuffix = true;
   boolean showText = true;
   boolean showColourText = false;
   boolean showBoxes = true;
@@ -53,14 +56,14 @@ public class AlignViewport
   boolean conservationColourSelected = false;
   boolean abovePIDThreshold = false;
 
-  SequenceGroup selectionGroup = new SequenceGroup();
+  SequenceGroup selectionGroup;
 
   int charHeight;
   int charWidth;
-  int chunkWidth;
-  int chunkHeight;
+  int wrappedWidth;
 
   Font font = new Font("SansSerif", Font.PLAIN, 10);
+  boolean validCharWidth = true;
   AlignmentI alignment;
 
   ColumnSelection colSel = new ColumnSelection();
@@ -74,6 +77,21 @@ public class AlignViewport
   boolean scaleLeftWrapped = true;
   boolean scaleRightWrapped = true;
 
+  // The following vector holds the features which are
+ // currently visible, in the correct order or rendering
+  Hashtable featuresDisplayed;
+
+
+  public Vector vconsensus;
+  AlignmentAnnotation consensus;
+  AlignmentAnnotation conservation;
+  AlignmentAnnotation quality;
+
+  boolean autocalculateConsensus = true;
+
+  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+  private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
 
   boolean ignoreGapsInConsensusCalculation = false;
 
@@ -91,7 +109,7 @@ public class AlignViewport
       String param = applet.getParameter("showFullId");
       if (param != null)
       {
-        showFullId = Boolean.valueOf(param).booleanValue();
+        showJVSuffix = Boolean.valueOf(param).booleanValue();
       }
 
       param = applet.getParameter("showAnnotation");
@@ -123,14 +141,34 @@ public class AlignViewport
     updateConservation();
     updateConsensus();
 
-    if (applet != null && applet.getParameter("defaultColour") != null)
+
+    if (applet != null)
     {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-          applet.getParameter("defaultColour"));
-      if (globalColourScheme != null)
+      String colour = applet.getParameter("defaultColour");
+
+      if(colour == null)
+      {
+        colour = applet.getParameter("userDefinedColour");
+        if(colour !=null)
+          colour = "User Defined";
+      }
+
+      if(colour != null)
       {
-        globalColourScheme.setConsensus(vconsensus);
+        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
+        if (globalColourScheme != null)
+        {
+          globalColourScheme.setConsensus(vconsensus);
+        }
       }
+
+      if(applet.getParameter("userDefinedColour")!=null)
+      {
+        ((UserColourScheme)globalColourScheme).parseAppletParameter(
+            applet.getParameter("userDefinedColour"));
+      }
+
+
     }
   }
 
@@ -139,15 +177,17 @@ public class AlignViewport
     showSequenceFeatures = b;
   }
 
-  public Vector vconsensus;
-  AlignmentAnnotation consensus;
-  AlignmentAnnotation conservation;
-  AlignmentAnnotation quality;
+  public boolean getShowSequenceFeatures()
+  {
+    return showSequenceFeatures;
+  }
 
-  public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
 
   public void updateConservation()
   {
+    if(alignment.isNucleotide())
+          return;
+
     Conservation cons = new jalview.analysis.Conservation("All",
         jalview.schemes.ResidueProperties.propHash, 3,
         alignment.getSequences(), 0,
@@ -217,7 +257,7 @@ public class AlignViewport
                                              annotations,
                                              0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
-                                             1);
+                                             AlignmentAnnotation.BAR_GRAPH);
       if (showConservation)
       {
         alignment.addAnnotation(conservation);
@@ -227,7 +267,7 @@ public class AlignViewport
                                         qannotations,
                                         cons.qualityRange[0].floatValue(),
                                         cons.qualityRange[1].floatValue(),
-                                        1);
+                                        AlignmentAnnotation.BAR_GRAPH);
       if (showQuality)
       {
         alignment.addAnnotation(quality);
@@ -290,7 +330,7 @@ public class AlignViewport
     if (consensus == null)
     {
       consensus = new AlignmentAnnotation("Consensus",
-                                          "PID", annotations, 0f, 100f, 1);
+                                          "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
       if (showConsensus)
       {
         alignment.addAnnotation(consensus);
@@ -301,6 +341,9 @@ public class AlignViewport
       consensus.annotations = annotations;
     }
 
+    if(globalColourScheme!=null)
+          globalColourScheme.setConsensus(vconsensus);
+
   }
 
   public SequenceGroup getSelectionGroup()
@@ -400,12 +443,17 @@ public class AlignViewport
     return endSeq;
   }
 
+  java.awt.Frame nullFrame;
   public void setFont(Font f)
   {
     font = f;
-    java.awt.Frame temp = new java.awt.Frame();
-    temp.addNotify();
-    java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);
+    if(nullFrame == null)
+    {
+      nullFrame = new java.awt.Frame();
+      nullFrame.addNotify();
+    }
+
+    java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
     setCharHeight(fm.getHeight());
     setCharWidth(fm.charWidth('M'));
   }
@@ -435,24 +483,14 @@ public class AlignViewport
     return charHeight;
   }
 
-  public void setChunkWidth(int w)
-  {
-    this.chunkWidth = w;
-  }
-
-  public int getChunkWidth()
-  {
-    return chunkWidth;
-  }
-
-  public void setChunkHeight(int h)
+  public void setWrappedWidth(int w)
   {
-    this.chunkHeight = h;
+    this.wrappedWidth = w;
   }
 
-  public int getChunkHeight()
+  public int getwrappedWidth()
   {
-    return chunkHeight;
+    return wrappedWidth;
   }
 
   public AlignmentI getAlignment()
@@ -543,32 +581,6 @@ public class AlignViewport
     return increment;
   }
 
-  public int getIndex(int y)
-  {
-    int y1 = 0;
-    int starty = getStartSeq();
-    int endy = getEndSeq();
-
-    for (int i = starty; i <= endy; i++)
-    {
-      if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null)
-      {
-        int y2 = y1 + getCharHeight();
-
-        if (y >= y1 && y <= y2)
-        {
-          return i;
-        }
-        y1 = y2;
-      }
-      else
-      {
-        return -1;
-      }
-    }
-    return -1;
-  }
-
   public ColumnSelection getColumnSelection()
   {
     return colSel;
@@ -599,14 +611,14 @@ public class AlignViewport
     return colourAppliesToAllGroups;
   }
 
-  public boolean getShowFullId()
+  public boolean getShowJVSuffix()
   {
-    return showFullId;
+    return showJVSuffix;
   }
 
-  public void setShowFullId(boolean b)
+  public void setShowJVSuffix(boolean b)
   {
-    showFullId = b;
+    showJVSuffix = b;
   }
 
   public boolean getShowAnnotation()
@@ -653,16 +665,50 @@ public class AlignViewport
   {
     ignoreGapsInConsensusCalculation = b;
     updateConsensus();
-    if (globalColourScheme!=null && globalColourScheme instanceof ResidueColourScheme)
+    if (globalColourScheme!=null)
     {
-      ( (ResidueColourScheme) globalColourScheme).setThreshold(
-          ( (ResidueColourScheme) globalColourScheme).getThreshold(),
+      globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
           ignoreGapsInConsensusCalculation);
 
     }
+  }
+
+  /**
+   * Property change listener for changes in alignment
+   *
+   * @param listener DOCUMENT ME!
+   */
+  public void addPropertyChangeListener(
+      java.beans.PropertyChangeListener listener)
+  {
+      changeSupport.addPropertyChangeListener(listener);
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param listener DOCUMENT ME!
+   */
+  public void removePropertyChangeListener(
+      java.beans.PropertyChangeListener listener)
+  {
+      changeSupport.removePropertyChangeListener(listener);
+  }
 
+  /**
+   * Property change listener for changes in alignment
+   *
+   * @param prop DOCUMENT ME!
+   * @param oldvalue DOCUMENT ME!
+   * @param newvalue DOCUMENT ME!
+   */
+  public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+  {
+      changeSupport.firePropertyChange(prop, oldvalue, newvalue);
   }
 
+
+
   public boolean getIgnoreGapsConsensus()
   {
     return ignoreGapsInConsensusCalculation;