int endRes;\r
int startSeq;\r
int endSeq;\r
- boolean showFullId = false;\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
- Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+ boolean validCharWidth;\r
+ int wrappedWidth;\r
+ Font font;\r
AlignmentI alignment;\r
ColumnSelection colSel = new ColumnSelection();\r
int threshold;\r
boolean scaleAboveWrapped = false;\r
boolean scaleLeftWrapped = true;\r
boolean scaleRightWrapped = true;\r
+ boolean hasHiddenColumns = false;\r
+ boolean hasHiddenRows = false;\r
+\r
+ boolean cursorMode = false;\r
+\r
+ // The following vector holds the features which are\r
+ // currently visible, in the correct order or rendering\r
+ Hashtable featuresDisplayed = null;\r
+\r
\r
/** DOCUMENT ME!! */\r
public Vector vconsensus;\r
AlignmentAnnotation consensus;\r
AlignmentAnnotation conservation;\r
AlignmentAnnotation quality;\r
+ boolean autoCalculateConsensus = true;\r
\r
/** DOCUMENT ME!! */\r
public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
\r
boolean ignoreGapsInConsensusCalculation = false;\r
\r
+ boolean isDataset = false;\r
+\r
+ boolean antiAlias = false;\r
+\r
+ boolean padGaps = 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
+ init();\r
+ }\r
+\r
+ void init()\r
+ {\r
this.startRes = 0;\r
- this.endRes = al.getWidth() - 1;\r
+ this.endRes = alignment.getWidth() - 1;\r
this.startSeq = 0;\r
- this.endSeq = al.getHeight() - 1;\r
+ this.endSeq = alignment.getHeight() - 1;\r
\r
- updateFromPreferences();\r
- }\r
+ antiAlias = Cache.getDefault("ANTI_ALIAS", false);\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateFromPreferences()\r
- {\r
- showFullId = Cache.getDefault("SHOW_FULL_ID", true);\r
+ showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);\r
showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);\r
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);\r
\r
showQuality = Cache.getDefault("SHOW_QUALITY", true);\r
showIdentity = Cache.getDefault("SHOW_IDENTITY", true);\r
\r
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);\r
+\r
+ padGaps = Cache.getDefault("PAD_GAPS", false);\r
+\r
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");\r
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;\r
String fontSize = Cache.getDefault("FONT_SIZE", "10");\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
* @param b DOCUMENT ME!\r
*/\r
- public void showSequenceFeatures(boolean b)\r
+ public void setShowSequenceFeatures(boolean b)\r
{\r
showSequenceFeatures = b;\r
}\r
\r
+ public boolean getShowSequenceFeatures()\r
+ {\r
+ return showSequenceFeatures;\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\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
ConsPercGaps + "% gaps",\r
annotations, 0f, // cons.qualityRange[0].floatValue(),\r
11f, // cons.qualityRange[1].floatValue()\r
- 1);\r
+ AlignmentAnnotation.BAR_GRAPH);\r
\r
if (showConservation)\r
{\r
qannotations,\r
cons.qualityRange[0].floatValue(),\r
cons.qualityRange[1].floatValue(),\r
- 1);\r
+ AlignmentAnnotation.BAR_GRAPH);\r
\r
if (showQuality)\r
{\r
}\r
catch (OutOfMemoryError error)\r
{\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
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\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
+ }\r
+ });\r
+\r
System.out.println("Conservation calculation: " + error);\r
System.gc();\r
\r
if (consensus == null)\r
{\r
consensus = new AlignmentAnnotation("Consensus", "PID",\r
- annotations, 0f, 100f, 1);\r
+ annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);\r
\r
if (showIdentity)\r
{\r
\r
}catch(OutOfMemoryError error)\r
{\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
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of memory calc45ulating consensus!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ javax.swing.JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
+\r
+\r
System.out.println("Consensus calculation: " + error);\r
System.gc();\r
}\r
java.awt.FontMetrics fm = c.getFontMetrics(font);\r
setCharHeight(fm.getHeight());\r
setCharWidth(fm.charWidth('M'));\r
+ validCharWidth = true;\r
}\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
/**\r
* DOCUMENT ME!\r
*\r
{\r
globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);\r
}\r
-\r
}\r
\r
public boolean getIgnoreGapsConsensus()\r
{\r
return ignoreGapsInConsensusCalculation;\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
+ public void hideSequence(SequenceI seq)\r
+ {\r
+ alignment.getHiddenSequences().hideSequence(seq);\r
+ hasHiddenRows = true;\r
+ }\r
+\r
+ public void showSequence(int index)\r
+ {\r
+ alignment.getHiddenSequences().showSequence(index);\r
+\r
+ if(alignment.getHiddenSequences().getSize()<1)\r
+ hasHiddenRows = false;\r
+ }\r
+\r
+ public int adjustForHiddenSeqs(int alignmentIndex)\r
+ {\r
+ return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff