int startSeq;\r
int endSeq;\r
\r
- boolean showFullId = true;\r
+ boolean showJVSuffix = true;\r
boolean showText = true;\r
boolean showColourText = false;\r
boolean showBoxes = true;\r
\r
int charHeight;\r
int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
+ int wrappedWidth;\r
\r
Font font = new Font("SansSerif", Font.PLAIN, 10);\r
AlignmentI alignment;\r
boolean scaleLeftWrapped = true;\r
boolean scaleRightWrapped = true;\r
\r
+ public Vector vconsensus;\r
+ AlignmentAnnotation consensus;\r
+ AlignmentAnnotation conservation;\r
+ AlignmentAnnotation quality;\r
+\r
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
+\r
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);\r
\r
boolean ignoreGapsInConsensusCalculation = false;\r
\r
String param = applet.getParameter("showFullId");\r
if (param != null)\r
{\r
- showFullId = Boolean.valueOf(param).booleanValue();\r
+ showJVSuffix = Boolean.valueOf(param).booleanValue();\r
}\r
\r
param = applet.getParameter("showAnnotation");\r
showSequenceFeatures = b;\r
}\r
\r
- public Vector vconsensus;\r
- AlignmentAnnotation consensus;\r
- AlignmentAnnotation conservation;\r
- AlignmentAnnotation quality;\r
-\r
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
\r
public void updateConservation()\r
{\r
+ if(alignment.isNucleotide())\r
+ return;\r
+\r
Conservation cons = new jalview.analysis.Conservation("All",\r
jalview.schemes.ResidueProperties.propHash, 3,\r
alignment.getSequences(), 0,\r
consensus.annotations = annotations;\r
}\r
\r
+ if(globalColourScheme!=null)\r
+ globalColourScheme.setConsensus(vconsensus);\r
+\r
}\r
\r
public SequenceGroup getSelectionGroup()\r
return charHeight;\r
}\r
\r
- public void setChunkWidth(int w)\r
+ public void setWrappedWidth(int w)\r
{\r
- this.chunkWidth = w;\r
+ this.wrappedWidth = w;\r
}\r
\r
- public int getChunkWidth()\r
+ public int getwrappedWidth()\r
{\r
- return chunkWidth;\r
- }\r
-\r
- public void setChunkHeight(int h)\r
- {\r
- this.chunkHeight = h;\r
- }\r
-\r
- public int getChunkHeight()\r
- {\r
- return chunkHeight;\r
+ return wrappedWidth;\r
}\r
\r
public AlignmentI getAlignment()\r
return colourAppliesToAllGroups;\r
}\r
\r
- public boolean getShowFullId()\r
+ public boolean getShowJVSuffix()\r
{\r
- return showFullId;\r
+ return showJVSuffix;\r
}\r
\r
- public void setShowFullId(boolean b)\r
+ public void setShowJVSuffix(boolean b)\r
{\r
- showFullId = b;\r
+ showJVSuffix = b;\r
}\r
\r
public boolean getShowAnnotation()\r
{\r
ignoreGapsInConsensusCalculation = b;\r
updateConsensus();\r
- if (globalColourScheme!=null && globalColourScheme instanceof ResidueColourScheme)\r
+ if (globalColourScheme!=null)\r
{\r
- ( (ResidueColourScheme) globalColourScheme).setThreshold(\r
- ( (ResidueColourScheme) globalColourScheme).getThreshold(),\r
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(),\r
ignoreGapsInConsensusCalculation);\r
\r
}\r
+ }\r
\r
+ /**\r
+ * Property change listener for changes in alignment\r
+ *\r
+ * @param listener DOCUMENT ME!\r
+ */\r
+ public void addPropertyChangeListener(\r
+ java.beans.PropertyChangeListener listener)\r
+ {\r
+ changeSupport.addPropertyChangeListener(listener);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param listener DOCUMENT ME!\r
+ */\r
+ public void removePropertyChangeListener(\r
+ java.beans.PropertyChangeListener listener)\r
+ {\r
+ changeSupport.removePropertyChangeListener(listener);\r
+ }\r
+\r
+ /**\r
+ * Property change listener for changes in alignment\r
+ *\r
+ * @param prop DOCUMENT ME!\r
+ * @param oldvalue DOCUMENT ME!\r
+ * @param newvalue DOCUMENT ME!\r
+ */\r
+ public void firePropertyChange(String prop, Object oldvalue, Object newvalue)\r
+ {\r
+ changeSupport.firePropertyChange(prop, oldvalue, newvalue);\r
+ }\r
+\r
+\r
+\r
public boolean getIgnoreGapsConsensus()\r
{\r
return ignoreGapsInConsensusCalculation;\r