// currently visible, in the correct order or rendering\r
Hashtable featuresDisplayed;\r
\r
+ boolean hasHiddenColumns = false;\r
+ boolean hasHiddenRows = false;\r
+ boolean showHiddenMarkers = true;\r
+\r
\r
public Vector vconsensus;\r
AlignmentAnnotation consensus;\r
\r
boolean ignoreGapsInConsensusCalculation = false;\r
\r
+ jalview.bin.JalviewLite applet;\r
+\r
public AlignViewport(AlignmentI al, JalviewLite applet)\r
{\r
+ this.applet = applet;\r
setAlignment(al);\r
this.startRes = 0;\r
this.endRes = al.getWidth() - 1;\r
return increment;\r
}\r
\r
+ public void setHiddenColumns(ColumnSelection colsel)\r
+ {\r
+ this.colSel = colsel;\r
+ if(colSel.getHiddenColumns()!=null)\r
+ hasHiddenColumns = true;\r
+ }\r
+\r
public ColumnSelection getColumnSelection()\r
{\r
return colSel;\r
{\r
return ignoreGapsInConsensusCalculation;\r
}\r
+ public void hideSelectedColumns()\r
+ {\r
+ if (colSel.size() < 1)\r
+ return;\r
+\r
+ colSel.hideSelectedColumns();\r
+ setSelectionGroup(null);\r
+\r
+ hasHiddenColumns = true;\r
+ }\r
+\r
+\r
+ public void hideColumns(int start, int end)\r
+ {\r
+ if(start==end)\r
+ colSel.hideColumns(start);\r
+ else\r
+ colSel.hideColumns(start, end);\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 showColumn(int col)\r
+ {\r
+ colSel.revealHiddenColumns(col);\r
+ if(colSel.getHiddenColumns()==null)\r
+ hasHiddenColumns = false;\r
+ }\r
+\r
+ public void showAllHiddenColumns()\r
+ {\r
+ colSel.revealAllHiddenColumns();\r
+ hasHiddenColumns = 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
+ * 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 jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)\r
+ {\r
+ CigarArray 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(); // inclusive for start and end in SeqCigar constructor\r
+ }\r
+ else\r
+ {\r
+ iSize = alignment.getHeight();\r
+ seqs = alignment.getSequencesArray();\r
+ end = alignment.getWidth()-1;\r
+ }\r
+ SeqCigar[] selseqs = new SeqCigar[iSize];\r
+ for(i=0; i<iSize; i++)\r
+ {\r
+ selseqs[i] = new SeqCigar(seqs[i], start, end);\r
+ }\r
+ selection=new CigarArray(selseqs);\r
+ // now construct the CigarArray operations\r
+ if (hasHiddenColumns) {\r
+ Vector regions = colSel.getHiddenColumns();\r
+ int [] region;\r
+ int hideStart, hideEnd;\r
+ int last=start;\r
+ for (int j = 0; last<end & j < regions.size(); j++)\r
+ {\r
+ region = (int[]) regions.elementAt(j);\r
+ hideStart = region[0];\r
+ hideEnd = region[1];\r
+ // edit hidden regions to selection range\r
+ if(hideStart<last) {\r
+ if (hideEnd > last)\r
+ {\r
+ hideStart = last;\r
+ } else\r
+ continue;\r
+ }\r
+\r
+ if (hideStart>end)\r
+ break;\r
+\r
+ if (hideEnd>end)\r
+ hideEnd=end;\r
+\r
+ if (hideStart>hideEnd)\r
+ break;\r
+ /**\r
+ * form operations...\r
+ */\r
+ if (last<hideStart)\r
+ selection.addOperation(CigarArray.M, hideStart-last);\r
+ selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);\r
+ last = hideEnd+1;\r
+ }\r
+ // Final match if necessary.\r
+ if (last<end)\r
+ selection.addOperation(CigarArray.M, end-last);\r
+ } else {\r
+ selection.addOperation(CigarArray.M, end-start);\r
+ }\r
+ return selection;\r
+ }\r
+ /**\r
+ * return a compact representation of the current alignment selection to\r
+ * pass to an analysis function\r
+ * @param selectedOnly boolean true to just return the selected view\r
+ * @return AlignmentView\r
+ */\r
+ jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {\r
+ // JBPNote:\r
+ // this is here because the AlignmentView constructor modifies the CigarArray\r
+ // object. Refactoring of Cigar and alignment view representation should\r
+ // be done to remove redundancy.\r
+ CigarArray aligview = getViewAsCigars(selectedOnly);\r
+ if (aligview!=null)\r
+ return new AlignmentView(aligview);\r
+ return null;\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
\r
}\r
git://source.jalview.org / jalview.git / blobdiff