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
+ boolean validCharWidth;\r
int wrappedWidth;\r
- Font font = new Font("SansSerif", Font.PLAIN, 10);\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
+ boolean showHiddenMarkers = true;\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
-\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
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
* @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
+\r
+ public void hideSelectedColumns()\r
+ {\r
+ if (colSel.selected.size() < 1)\r
+ return;\r
+\r
+ while (colSel.selected.size() > 0)\r
+ {\r
+ int column = ( (Integer) colSel.selected.firstElement()).intValue();\r
+ colSel.hideColumns(column);\r
+ }\r
+ setSelectionGroup(null);\r
+ hasHiddenColumns = true;\r
+ }\r
+\r
+\r
+ public void hideColumns(int start, int end)\r
+ {\r
+ if(start==end)\r
+ end++;\r
+\r
+ for(int i=start; i<end; i++)\r
+ {\r
+ colSel.addElement(i);\r
+ colSel.hideColumns(i);\r
+ }\r
+\r
+ setSelectionGroup(null);\r
+ hasHiddenColumns = true;\r
+ }\r
+\r
+ public void hideSequence(SequenceI seq)\r
+ {\r
+ if(seq!=null)\r
+ {\r
+ alignment.getHiddenSequences().hideSequence(seq);\r
+ hasHiddenRows = true;\r
+ }\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 void showAllHiddenSeqs()\r
+ {\r
+ if(alignment.getHiddenSequences().getSize()>0)\r
+ {\r
+ alignment.getHiddenSequences().showAll();\r
+ hasHiddenRows = false;\r
+ }\r
+ }\r
+\r
+ public int adjustForHiddenSeqs(int alignmentIndex)\r
+ {\r
+ return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);\r
+ }\r
+\r
+ /**\r
+ * This method returns the a new SequenceI [] with\r
+ * the selection sequence and start and end points adjusted\r
+ * @return String[]\r
+ */\r
+ public SequenceI[] getSelectionAsNewSequence()\r
+ {\r
+ SequenceI[] sequences;\r
+\r
+ if (selectionGroup == null)\r
+ sequences = alignment.getSequencesArray();\r
+ else\r
+ sequences = selectionGroup.getSelectionAsNewSequences(alignment);\r
+\r
+ return sequences;\r
+ }\r
+\r
+\r
+ /**\r
+ * This method returns the visible alignment as text, as\r
+ * seen on the GUI, ie if columns are hidden they will not\r
+ * be returned in the result.\r
+ * Use this for calculating trees, PCA, redundancy etc on views\r
+ * which contain hidden columns.\r
+ * @return String[]\r
+ */\r
+ public String [] getViewAsString(boolean selectedRegionOnly)\r
+ {\r
+ String [] selection = null;\r
+ SequenceI [] seqs= null;\r
+ int i, iSize;\r
+ int start = 0, end = 0;\r
+ if(selectedRegionOnly && selectionGroup!=null)\r
+ {\r
+ iSize = selectionGroup.getSize(false);\r
+ seqs = selectionGroup.getSequencesInOrder(alignment);\r
+ start = selectionGroup.getStartRes();\r
+ end = selectionGroup.getEndRes()+1;\r
+ }\r
+ else\r
+ {\r
+ iSize = alignment.getHeight();\r
+ seqs = alignment.getSequencesArray();\r
+ end = alignment.getWidth();\r
+ }\r
+\r
+ selection = new String[iSize];\r
+\r
+\r
+ for(i=0; i<iSize; i++)\r
+ {\r
+ if (hasHiddenColumns)\r
+ {\r
+ StringBuffer visibleSeq = new StringBuffer();\r
+ Vector regions = colSel.getHiddenColumns();\r
+\r
+ int blockStart = start, blockEnd=end;\r
+ int [] region;\r
+ int hideStart, hideEnd;\r
+\r
+ for (int j = 0; j < regions.size(); j++)\r
+ {\r
+ region = (int[]) regions.elementAt(j);\r
+ hideStart = region[0];\r
+ hideEnd = region[1];\r
+\r
+ if(hideStart < start)\r
+ {\r
+ continue;\r
+ }\r
+\r
+ blockStart = Math.min(blockStart, hideEnd+1);\r
+ blockEnd = Math.min(blockEnd, hideStart);\r
+\r
+ if(blockStart>blockEnd)\r
+ {\r
+ break;\r
+ }\r
+\r
+\r
+ visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));\r
+\r
+ blockStart = hideEnd+1;\r
+ blockEnd = end;\r
+ }\r
+\r
+ if(end>blockStart)\r
+ visibleSeq.append(seqs[i].getSequence(blockStart, end));\r
+\r
+ selection[i] = visibleSeq.toString();\r
+ }\r
+ else\r
+ {\r
+ selection[i] = seqs[i].getSequence(start, end);\r
+ }\r
+ }\r
+\r
+ return selection;\r
+ }\r
+\r
+ public boolean getShowHiddenMarkers()\r
+ {\r
+ return showHiddenMarkers;\r
+ }\r
+\r
+ public void setShowHiddenMarkers(boolean show)\r
+ {\r
+ showHiddenMarkers = show;\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff