int endRes;\r
int startSeq;\r
int endSeq;\r
- boolean showFullId = false;\r
+ boolean showDBPrefix = true;\r
+ boolean showJVSuffix = true;\r
boolean showText = true;\r
boolean showColourText = false;\r
boolean showBoxes = true;\r
SequenceGroup selectionGroup;\r
int charHeight;\r
int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
+ int wrappedWidth;\r
Font font = new Font("SansSerif", Font.PLAIN, 10);\r
AlignmentI alignment;\r
ColumnSelection colSel = new ColumnSelection();\r
\r
boolean ignoreGapsInConsensusCalculation = false;\r
\r
+ boolean showTranslation = false;\r
+\r
+ boolean isDataset = false;\r
+\r
+\r
+ public AlignViewport(AlignmentI al, boolean dataset)\r
+ {\r
+ isDataset = dataset;\r
+ setAlignment(al);\r
+ init();\r
+ }\r
/**\r
* Creates a new AlignViewport object.\r
*\r
public AlignViewport(AlignmentI al)\r
{\r
setAlignment(al);\r
- this.startRes = 0;\r
- this.endRes = al.getWidth() - 1;\r
- this.startSeq = 0;\r
- this.endSeq = al.getHeight() - 1;\r
-\r
- updateFromPreferences();\r
+ init();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateFromPreferences()\r
+ void init()\r
{\r
- showFullId = Cache.getDefault("SHOW_FULL_ID", true);\r
+ this.startRes = 0;\r
+ this.endRes = alignment.getWidth() - 1;\r
+ this.startSeq = 0;\r
+ this.endSeq = alignment.getHeight() - 1;\r
+\r
+ showDBPrefix = Cache.getDefault("SHOW_DBPREFIX", true);\r
+ showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);\r
showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);\r
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);\r
\r
\r
// We must set conservation and consensus before setting colour,\r
// as Blosum and Clustal require this to be done\r
- updateConservation();\r
- updateConsensus();\r
+ if(vconsensus==null && !isDataset)\r
+ {\r
+ updateConservation();\r
+ updateConsensus();\r
+ }\r
\r
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)\r
{\r
*/\r
public void updateConservation()\r
{\r
+ if(alignment.isNucleotide())\r
+ return;\r
+\r
try{\r
Conservation cons = new jalview.analysis.Conservation("All",\r
jalview.schemes.ResidueProperties.propHash, 3,\r
quality.annotations = qannotations;\r
quality.graphMax = cons.qualityRange[1].floatValue();\r
}\r
- }catch(OutOfMemoryError error)\r
+ }\r
+ catch (OutOfMemoryError error)\r
{\r
- System.out.println("Out of memory calculating conservation.");\r
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of memory calculating conservation!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ javax.swing.JOptionPane.WARNING_MESSAGE);\r
+ System.out.println("Conservation calculation: " + error);\r
System.gc();\r
+\r
}\r
}\r
\r
\r
}catch(OutOfMemoryError error)\r
{\r
- System.out.println("Out of memory calculating consensus.");\r
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of memory calculating consensus!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ javax.swing.JOptionPane.WARNING_MESSAGE);\r
+ System.out.println("Consensus calculation: " + error);\r
System.gc();\r
}\r
\r
*\r
* @param w DOCUMENT ME!\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
/**\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public int getChunkWidth()\r
+ public int getWrappedWidth()\r
{\r
- return chunkWidth;\r
+ return wrappedWidth;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param h DOCUMENT ME!\r
- */\r
- public void setChunkHeight(int h)\r
- {\r
- this.chunkHeight = h;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getChunkHeight()\r
- {\r
- return chunkHeight;\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public boolean getShowFullId()\r
+ public boolean getShowJVSuffix()\r
{\r
- return showFullId;\r
+ return showJVSuffix;\r
}\r
\r
/**\r
*\r
* @param b DOCUMENT ME!\r
*/\r
- public void setShowFullId(boolean b)\r
+ public void setShowJVSuffix(boolean b)\r
{\r
- showFullId = b;\r
+ showJVSuffix = b;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getShowDBPrefix()\r
+ {\r
+ return showDBPrefix;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void setShowDBPrefix(boolean b)\r
+ {\r
+ showDBPrefix = b;\r
}\r
\r
/**\r
{\r
return ignoreGapsInConsensusCalculation;\r
}\r
+\r
+ public void showTranslation(boolean b)\r
+ {\r
+ this.showTranslation = b;\r
+ }\r
+\r
+ public boolean getShowTranslation()\r
+ {\r
+ return showTranslation;\r
+ }\r
+\r
+ public void setDataset(boolean b)\r
+ {\r
+ isDataset = b;\r
+ }\r
+\r
+ public boolean isDataset()\r
+ {\r
+ return isDataset;\r
+ }\r
}\r