-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.bin.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-\r
-public class AlignViewport\r
-{\r
- int startRes;\r
- int endRes;\r
-\r
- int startSeq;\r
- int endSeq;\r
-\r
-\r
- boolean cursorMode = false;\r
-\r
- boolean showJVSuffix = true;\r
- boolean showText = true;\r
- boolean showColourText = false;\r
- boolean showBoxes = true;\r
- boolean wrapAlignment = false;\r
- boolean renderGaps = true;\r
- boolean showSequenceFeatures = false;\r
- boolean showAnnotation = true;\r
- boolean showConservation = true;\r
- boolean showQuality = true;\r
- boolean showConsensus = true;\r
- boolean upperCasebold = false;\r
-\r
- boolean colourAppliesToAllGroups = true;\r
- ColourSchemeI globalColourScheme = null;\r
- boolean conservationColourSelected = false;\r
- boolean abovePIDThreshold = false;\r
-\r
- SequenceGroup selectionGroup;\r
-\r
- int charHeight;\r
- int charWidth;\r
- int wrappedWidth;\r
-\r
- Font font = new Font("SansSerif", Font.PLAIN, 10);\r
- boolean validCharWidth = true;\r
- AlignmentI alignment;\r
-\r
- ColumnSelection colSel = new ColumnSelection();\r
-\r
- int threshold;\r
- int increment;\r
-\r
- NJTree currentTree = null;\r
-\r
- boolean scaleAboveWrapped = true;\r
- boolean scaleLeftWrapped = true;\r
- boolean scaleRightWrapped = true;\r
-\r
- // The following vector holds the features which are\r
- // currently visible, in the correct order or rendering\r
- public Hashtable featuresDisplayed;\r
-\r
- boolean hasHiddenColumns = false;\r
- boolean hasHiddenRows = false;\r
- boolean showHiddenMarkers = true;\r
-\r
-\r
- public Hashtable [] hconsensus;\r
- AlignmentAnnotation consensus;\r
- AlignmentAnnotation conservation;\r
- AlignmentAnnotation quality;\r
-\r
- boolean autocalculateConsensus = true;\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
- jalview.bin.JalviewLite applet;\r
-\r
- boolean MAC = false;\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
- this.startSeq = 0;\r
- this.endSeq = al.getHeight() - 1;\r
- setFont(font);\r
-\r
- if(System.getProperty("os.name").startsWith("Mac"))\r
- MAC = true;\r
-\r
- if (applet != null)\r
- {\r
- String param = applet.getParameter("showFullId");\r
- if (param != null)\r
- {\r
- showJVSuffix = Boolean.valueOf(param).booleanValue();\r
- }\r
-\r
- param = applet.getParameter("showAnnotation");\r
- if (param != null)\r
- {\r
- showAnnotation = Boolean.valueOf(param).booleanValue();\r
- }\r
-\r
- param = applet.getParameter("showConservation");\r
- if (param != null)\r
- {\r
- showConservation = Boolean.valueOf(param).booleanValue();\r
- }\r
-\r
- param = applet.getParameter("showQuality");\r
- if (param != null)\r
- {\r
- showQuality = Boolean.valueOf(param).booleanValue();\r
- }\r
-\r
- param = applet.getParameter("showConsensus");\r
- if (param != null)\r
- {\r
- showConsensus = Boolean.valueOf(param).booleanValue();\r
- }\r
-\r
- param = applet.getParameter("upperCase");\r
- if (param != null)\r
- {\r
- if(param.equalsIgnoreCase("bold"))\r
- upperCasebold = true;\r
- }\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
-\r
-\r
- if (applet != null)\r
- {\r
- String colour = applet.getParameter("defaultColour");\r
-\r
- if(colour == null)\r
- {\r
- colour = applet.getParameter("userDefinedColour");\r
- if(colour !=null)\r
- colour = "User Defined";\r
- }\r
-\r
- if(colour != null)\r
- {\r
- globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);\r
- if (globalColourScheme != null)\r
- {\r
- globalColourScheme.setConsensus(hconsensus);\r
- }\r
- }\r
-\r
- if(applet.getParameter("userDefinedColour")!=null)\r
- {\r
- ((UserColourScheme)globalColourScheme).parseAppletParameter(\r
- applet.getParameter("userDefinedColour"));\r
- }\r
-\r
-\r
- }\r
- }\r
-\r
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\r
- }\r
-\r
- public boolean getShowSequenceFeatures()\r
- {\r
- return showSequenceFeatures;\r
- }\r
-\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
- alignment.getWidth() - 1);\r
- cons.calculate();\r
- cons.verdict(false, ConsPercGaps);\r
- cons.findQuality();\r
- int alWidth = alignment.getWidth();\r
- Annotation[] annotations = new Annotation[alWidth];\r
- Annotation[] qannotations = new Annotation[alWidth];\r
- String sequence = cons.getConsSequence().getSequence();\r
- float minR, minG, minB, maxR, maxG, maxB;\r
- minR = 0.3f;\r
- minG = 0.0f;\r
- minB = 0f;\r
- maxR = 1.0f - minR;\r
- maxG = 0.9f - minG;\r
- maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
- float min = 0f;\r
- float max = 11f;\r
- float qmin = cons.qualityRange[0].floatValue();\r
- float qmax = cons.qualityRange[1].floatValue();\r
-\r
- for (int i = 0; i < alWidth; i++)\r
- {\r
- float value = 0;\r
- try\r
- {\r
- value = Integer.parseInt(sequence.charAt(i) + "");\r
- }\r
- catch (Exception ex)\r
- {\r
- if (sequence.charAt(i) == '*')\r
- {\r
- value = 11;\r
- }\r
- if (sequence.charAt(i) == '+')\r
- {\r
- value = 10;\r
- }\r
- }\r
- float vprop = value - min;\r
- vprop /= max;\r
-\r
- annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- "", ' ', value,\r
- new Color(minR + maxR * vprop,\r
- minG + maxG * vprop,\r
- minB + maxB * vprop));\r
- // Quality calc\r
- value = ( (Double) cons.quality.elementAt(i)).floatValue();\r
- vprop = value - qmin;\r
- vprop /= qmax;\r
- qannotations[i] = new Annotation(" ",\r
- String.valueOf(value), ' ', value,\r
- new\r
- Color(minR + maxR * vprop,\r
- minG + maxG * vprop,\r
- minB + maxB * vprop));\r
- }\r
-\r
- if (conservation == null)\r
- {\r
- conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than " +\r
- ConsPercGaps + "% gaps",\r
- annotations,\r
- 0f, // cons.qualityRange[0].floatValue(),\r
- 11f, // cons.qualityRange[1].floatValue()\r
- AlignmentAnnotation.BAR_GRAPH);\r
- if (showConservation)\r
- {\r
- alignment.addAnnotation(conservation);\r
- }\r
- quality = new AlignmentAnnotation("Quality",\r
- "Alignment Quality based on Blosum62 scores",\r
- qannotations,\r
- cons.qualityRange[0].floatValue(),\r
- cons.qualityRange[1].floatValue(),\r
- AlignmentAnnotation.BAR_GRAPH);\r
- if (showQuality)\r
- {\r
- alignment.addAnnotation(quality);\r
- }\r
- }\r
- else\r
- {\r
- conservation.annotations = annotations;\r
- quality.annotations = qannotations;\r
- quality.graphMax = cons.qualityRange[1].floatValue();\r
- }\r
-\r
- }\r
-\r
- public void updateConsensus()\r
- {\r
- // this routine prevents vconsensus becoming a new object each time\r
- // consenus is calculated. Important for speed of Blosum62\r
- // and PID colouring of alignment\r
- int aWidth = alignment.getWidth();\r
-\r
- Annotation[] annotations = new Annotation[aWidth];\r
-\r
- hconsensus = new Hashtable[aWidth];\r
- AAFrequency.calculate(alignment.getSequencesArray(),\r
- 0, aWidth,\r
- hconsensus);\r
-\r
- for (int i = 0; i < aWidth; i++)\r
- {\r
- float value = 0;\r
- if(ignoreGapsInConsensusCalculation)\r
- value = ((Float)hconsensus[i].get("pid_nogaps")).floatValue();\r
- else\r
- value = ((Float)hconsensus[i].get("pid_gaps")).floatValue();\r
-\r
- String maxRes = hconsensus[i].get("maxResidue").toString();\r
- String mouseOver = hconsensus[i].get("maxResidue") + " ";\r
- if (maxRes.length() > 1)\r
- {\r
- mouseOver = "[" + maxRes + "] ";\r
- maxRes = "+";\r
- }\r
-\r
-\r
- mouseOver += (int) value + "%";\r
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
-\r
- }\r
-\r
- if (consensus == null)\r
- {\r
- consensus = new AlignmentAnnotation("Consensus",\r
- "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);\r
- if (showConsensus)\r
- {\r
- alignment.addAnnotation(consensus);\r
- }\r
- }\r
- else\r
- {\r
- consensus.annotations = annotations;\r
- }\r
-\r
- if(globalColourScheme!=null)\r
- globalColourScheme.setConsensus(hconsensus);\r
-\r
- }\r
- /**\r
- * get the consensus sequence as displayed under the PID consensus annotation row.\r
- * @return consensus sequence as a new sequence object\r
- */\r
- /**\r
- * get the consensus sequence as displayed under the PID consensus annotation row.\r
- * @return consensus sequence as a new sequence object\r
- */\r
- public SequenceI getConsensusSeq() {\r
- if (consensus==null)\r
- updateConsensus();\r
- if (consensus==null)\r
- return null;\r
- StringBuffer seqs=new StringBuffer();\r
- for (int i=0; i<consensus.annotations.length; i++) {\r
- if (consensus.annotations[i]!=null) {\r
- if (consensus.annotations[i].description.charAt(0) == '[')\r
- seqs.append(consensus.annotations[i].description.charAt(1));\r
- else\r
- seqs.append(consensus.annotations[i].displayCharacter);\r
- }\r
- }\r
- SequenceI sq = new Sequence("Consensus", seqs.toString());\r
- sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));\r
- return sq;\r
- }\r
- public SequenceGroup getSelectionGroup()\r
- {\r
- return selectionGroup;\r
- }\r
-\r
- public void setSelectionGroup(SequenceGroup sg)\r
- {\r
- selectionGroup = sg;\r
- }\r
-\r
- public boolean getConservationSelected()\r
- {\r
- return conservationColourSelected;\r
- }\r
-\r
- public void setConservationSelected(boolean b)\r
- {\r
- conservationColourSelected = b;\r
- }\r
-\r
- public boolean getAbovePIDThreshold()\r
- {\r
- return abovePIDThreshold;\r
- }\r
-\r
- public void setAbovePIDThreshold(boolean b)\r
- {\r
- abovePIDThreshold = b;\r
- }\r
-\r
- public int getStartRes()\r
- {\r
- return startRes;\r
- }\r
-\r
- public int getEndRes()\r
- {\r
- return endRes;\r
- }\r
-\r
- public int getStartSeq()\r
- {\r
- return startSeq;\r
- }\r
-\r
- public void setGlobalColourScheme(ColourSchemeI cs)\r
- {\r
- globalColourScheme = cs;\r
- }\r
-\r
- public ColourSchemeI getGlobalColourScheme()\r
- {\r
- return globalColourScheme;\r
- }\r
-\r
- public void setStartRes(int res)\r
- {\r
- this.startRes = res;\r
- }\r
-\r
- public void setStartSeq(int seq)\r
- {\r
- this.startSeq = seq;\r
- }\r
-\r
- public void setEndRes(int res)\r
- {\r
- if (res > alignment.getWidth() - 1)\r
- {\r
- // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth() - 1;\r
- }\r
- if (res < 0)\r
- {\r
- res = 0;\r
- }\r
- this.endRes = res;\r
- }\r
-\r
- public void setEndSeq(int seq)\r
- {\r
- if (seq > alignment.getHeight())\r
- {\r
- seq = alignment.getHeight();\r
- }\r
- if (seq < 0)\r
- {\r
- seq = 0;\r
- }\r
- this.endSeq = seq;\r
- }\r
-\r
- public int getEndSeq()\r
- {\r
- return endSeq;\r
- }\r
-\r
- java.awt.Frame nullFrame;\r
- public void setFont(Font f)\r
- {\r
- font = f;\r
- if(nullFrame == null)\r
- {\r
- nullFrame = new java.awt.Frame();\r
- nullFrame.addNotify();\r
- }\r
-\r
- java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);\r
- setCharHeight(fm.getHeight());\r
- charWidth = fm.charWidth('M');\r
-\r
- if(upperCasebold)\r
- {\r
- Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());\r
- fm = nullFrame.getGraphics().getFontMetrics(f2);\r
- charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;\r
- }\r
- }\r
-\r
- public Font getFont()\r
- {\r
- return font;\r
- }\r
-\r
- public int getCharWidth()\r
- {\r
- return charWidth;\r
- }\r
-\r
- public void setCharHeight(int h)\r
- {\r
- this.charHeight = h;\r
- }\r
-\r
- public int getCharHeight()\r
- {\r
- return charHeight;\r
- }\r
-\r
- public void setWrappedWidth(int w)\r
- {\r
- this.wrappedWidth = w;\r
- }\r
-\r
- public int getwrappedWidth()\r
- {\r
- return wrappedWidth;\r
- }\r
-\r
- public AlignmentI getAlignment()\r
- {\r
- return alignment;\r
- }\r
-\r
- public void setAlignment(AlignmentI align)\r
- {\r
- this.alignment = align;\r
- }\r
-\r
- public void setWrapAlignment(boolean state)\r
- {\r
- wrapAlignment = state;\r
- }\r
-\r
- public void setShowText(boolean state)\r
- {\r
- showText = state;\r
- }\r
-\r
- public void setRenderGaps(boolean state)\r
- {\r
- renderGaps = state;\r
- }\r
-\r
- public boolean getColourText()\r
- {\r
- return showColourText;\r
- }\r
-\r
- public void setColourText(boolean state)\r
- {\r
- showColourText = state;\r
- }\r
-\r
- public void setShowBoxes(boolean state)\r
- {\r
- showBoxes = state;\r
- }\r
-\r
- public boolean getWrapAlignment()\r
- {\r
- return wrapAlignment;\r
- }\r
-\r
- public boolean getShowText()\r
- {\r
- return showText;\r
- }\r
-\r
- public boolean getShowBoxes()\r
- {\r
- return showBoxes;\r
- }\r
-\r
- public char getGapCharacter()\r
- {\r
- return getAlignment().getGapCharacter();\r
- }\r
-\r
- public void setGapCharacter(char gap)\r
- {\r
- if (getAlignment() != null)\r
- {\r
- getAlignment().setGapCharacter(gap);\r
- }\r
- }\r
-\r
- public void setThreshold(int thresh)\r
- {\r
- threshold = thresh;\r
- }\r
-\r
- public int getThreshold()\r
- {\r
- return threshold;\r
- }\r
-\r
- public void setIncrement(int inc)\r
- {\r
- increment = inc;\r
- }\r
-\r
- public int getIncrement()\r
- {\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
-\r
- public void resetSeqLimits(int height)\r
- {\r
- setEndSeq(height / getCharHeight());\r
- }\r
-\r
- public void setCurrentTree(NJTree tree)\r
- {\r
- currentTree = tree;\r
- }\r
-\r
- public NJTree getCurrentTree()\r
- {\r
- return currentTree;\r
- }\r
-\r
- public void setColourAppliesToAllGroups(boolean b)\r
- {\r
- colourAppliesToAllGroups = b;\r
- }\r
-\r
- public boolean getColourAppliesToAllGroups()\r
- {\r
- return colourAppliesToAllGroups;\r
- }\r
-\r
- public boolean getShowJVSuffix()\r
- {\r
- return showJVSuffix;\r
- }\r
-\r
- public void setShowJVSuffix(boolean b)\r
- {\r
- showJVSuffix = b;\r
- }\r
-\r
- public boolean getShowAnnotation()\r
- {\r
- return showAnnotation;\r
- }\r
-\r
- public void setShowAnnotation(boolean b)\r
- {\r
- showAnnotation = b;\r
- }\r
-\r
- public boolean getScaleAboveWrapped()\r
- {\r
- return scaleAboveWrapped;\r
- }\r
-\r
- public boolean getScaleLeftWrapped()\r
- {\r
- return scaleLeftWrapped;\r
- }\r
-\r
- public boolean getScaleRightWrapped()\r
- {\r
- return scaleRightWrapped;\r
- }\r
-\r
- public void setScaleAboveWrapped(boolean b)\r
- {\r
- scaleAboveWrapped = b;\r
- }\r
-\r
- public void setScaleLeftWrapped(boolean b)\r
- {\r
- scaleLeftWrapped = b;\r
- }\r
-\r
- public void setScaleRightWrapped(boolean b)\r
- {\r
- scaleRightWrapped = b;\r
- }\r
-\r
- public void setIgnoreGapsConsensus(boolean b)\r
- {\r
- ignoreGapsInConsensusCalculation = b;\r
- updateConsensus();\r
- if (globalColourScheme!=null)\r
- {\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
- }\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
- public void invertColumnSelection()\r
- {\r
- int column;\r
- for (int i = 0; i < alignment.getWidth(); i++)\r
- {\r
- column = i;\r
-\r
- if (colSel.contains(column))\r
- colSel.removeElement(column);\r
- else\r
- colSel.addElement(column);\r
-\r
- }\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
-\r
- hasHiddenColumns = true;\r
- }\r
-\r
- public void hideAllSelectedSeqs()\r
- {\r
- if (selectionGroup == null)\r
- return;\r
-\r
- SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);\r
-\r
- hideSequence(seqs);\r
-\r
- setSelectionGroup(null);\r
- }\r
-\r
- public void hideSequence(SequenceI [] seq)\r
- {\r
- if(seq!=null)\r
- {\r
- for (int i = 0; i < seq.length; i++)\r
- alignment.getHiddenSequences().hideSequence(seq[i]);\r
-\r
- hasHiddenRows = true;\r
- firePropertyChange("alignment", null, alignment.getSequences());\r
- }\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
- if(selectionGroup==null)\r
- {\r
- selectionGroup = new SequenceGroup();\r
- selectionGroup.setEndRes(alignment.getWidth()-1);\r
- }\r
- Vector tmp = alignment.getHiddenSequences().showAll();\r
- for(int t=0; t<tmp.size(); t++)\r
- {\r
- selectionGroup.addSequence(\r
- (SequenceI)tmp.elementAt(t), false\r
- );\r
- }\r
- firePropertyChange("alignment", null, alignment.getSequences());\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+1);\r
- } else {\r
- selection.addOperation(CigarArray.M, end-start+1);\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+public class AlignViewport
+{
+ int startRes;
+ int endRes;
+
+ int startSeq;
+ int endSeq;
+
+
+ boolean cursorMode = false;
+
+ boolean showJVSuffix = true;
+ boolean showText = true;
+ boolean showColourText = false;
+ boolean showBoxes = true;
+ boolean wrapAlignment = false;
+ boolean renderGaps = true;
+ boolean showSequenceFeatures = false;
+ boolean showAnnotation = true;
+ boolean showConservation = true;
+ boolean showQuality = true;
+ boolean showConsensus = true;
+ boolean upperCasebold = false;
+
+ boolean colourAppliesToAllGroups = true;
+ ColourSchemeI globalColourScheme = null;
+ boolean conservationColourSelected = false;
+ boolean abovePIDThreshold = false;
+
+ SequenceGroup selectionGroup;
+
+ int charHeight;
+ int charWidth;
+ int wrappedWidth;
+
+ Font font = new Font("SansSerif", Font.PLAIN, 10);
+ boolean validCharWidth = true;
+ AlignmentI alignment;
+
+ ColumnSelection colSel = new ColumnSelection();
+
+ int threshold;
+ int increment;
+
+ NJTree currentTree = null;
+
+ boolean scaleAboveWrapped = true;
+ boolean scaleLeftWrapped = true;
+ boolean scaleRightWrapped = true;
+
+ // The following vector holds the features which are
+ // currently visible, in the correct order or rendering
+ public Hashtable featuresDisplayed;
+
+ boolean hasHiddenColumns = false;
+ boolean hasHiddenRows = false;
+ boolean showHiddenMarkers = true;
+
+
+ public Hashtable [] hconsensus;
+ AlignmentAnnotation consensus;
+ AlignmentAnnotation conservation;
+ AlignmentAnnotation quality;
+
+ boolean autocalculateConsensus = true;
+
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);
+
+ boolean ignoreGapsInConsensusCalculation = false;
+
+ jalview.bin.JalviewLite applet;
+
+ boolean MAC = false;
+
+ public AlignViewport(AlignmentI al, JalviewLite applet)
+ {
+ this.applet = applet;
+ setAlignment(al);
+ this.startRes = 0;
+ this.endRes = al.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = al.getHeight() - 1;
+ setFont(font);
+
+ if(System.getProperty("os.name").startsWith("Mac"))
+ MAC = true;
+
+ if (applet != null)
+ {
+ String param = applet.getParameter("showFullId");
+ if (param != null)
+ {
+ showJVSuffix = Boolean.valueOf(param).booleanValue();
+ }
+
+ param = applet.getParameter("showAnnotation");
+ if (param != null)
+ {
+ showAnnotation = Boolean.valueOf(param).booleanValue();
+ }
+
+ param = applet.getParameter("showConservation");
+ if (param != null)
+ {
+ showConservation = Boolean.valueOf(param).booleanValue();
+ }
+
+ param = applet.getParameter("showQuality");
+ if (param != null)
+ {
+ showQuality = Boolean.valueOf(param).booleanValue();
+ }
+
+ param = applet.getParameter("showConsensus");
+ if (param != null)
+ {
+ showConsensus = Boolean.valueOf(param).booleanValue();
+ }
+
+ param = applet.getParameter("upperCase");
+ if (param != null)
+ {
+ if(param.equalsIgnoreCase("bold"))
+ upperCasebold = true;
+ }
+
+ }
+ // We must set conservation and consensus before setting colour,
+ // as Blosum and Clustal require this to be done
+ updateConservation();
+ updateConsensus();
+
+
+ if (applet != null)
+ {
+ String colour = applet.getParameter("defaultColour");
+
+ if(colour == null)
+ {
+ colour = applet.getParameter("userDefinedColour");
+ if(colour !=null)
+ colour = "User Defined";
+ }
+
+ if(colour != null)
+ {
+ globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
+ }
+
+ if(applet.getParameter("userDefinedColour")!=null)
+ {
+ ((UserColourScheme)globalColourScheme).parseAppletParameter(
+ applet.getParameter("userDefinedColour"));
+ }
+
+
+ }
+ }
+
+ public void showSequenceFeatures(boolean b)
+ {
+ showSequenceFeatures = b;
+ }
+
+ public boolean getShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+
+ public void updateConservation()
+ {
+ if(alignment.isNucleotide())
+ return;
+
+ Conservation cons = new jalview.analysis.Conservation("All",
+ jalview.schemes.ResidueProperties.propHash, 3,
+ alignment.getSequences(), 0,
+ alignment.getWidth() - 1);
+ cons.calculate();
+ cons.verdict(false, ConsPercGaps);
+ cons.findQuality();
+ int alWidth = alignment.getWidth();
+ Annotation[] annotations = new Annotation[alWidth];
+ Annotation[] qannotations = new Annotation[alWidth];
+ String sequence = cons.getConsSequence().getSequence();
+ float minR, minG, minB, maxR, maxG, maxB;
+ minR = 0.3f;
+ minG = 0.0f;
+ minB = 0f;
+ maxR = 1.0f - minR;
+ maxG = 0.9f - minG;
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
+ float min = 0f;
+ float max = 11f;
+ float qmin = cons.qualityRange[0].floatValue();
+ float qmax = cons.qualityRange[1].floatValue();
+
+ for (int i = 0; i < alWidth; i++)
+ {
+ float value = 0;
+ try
+ {
+ value = Integer.parseInt(sequence.charAt(i) + "");
+ }
+ catch (Exception ex)
+ {
+ if (sequence.charAt(i) == '*')
+ {
+ value = 11;
+ }
+ if (sequence.charAt(i) == '+')
+ {
+ value = 10;
+ }
+ }
+ float vprop = value - min;
+ vprop /= max;
+
+ annotations[i] = new Annotation(sequence.charAt(i) + "",
+ "", ' ', value,
+ new Color(minR + maxR * vprop,
+ minG + maxG * vprop,
+ minB + maxB * vprop));
+ // Quality calc
+ value = ( (Double) cons.quality.elementAt(i)).floatValue();
+ vprop = value - qmin;
+ vprop /= qmax;
+ qannotations[i] = new Annotation(" ",
+ String.valueOf(value), ' ', value,
+ new
+ Color(minR + maxR * vprop,
+ minG + maxG * vprop,
+ minB + maxB * vprop));
+ }
+
+ if (conservation == null)
+ {
+ conservation = new AlignmentAnnotation("Conservation",
+ "Conservation of total alignment less than " +
+ ConsPercGaps + "% gaps",
+ annotations,
+ 0f, // cons.qualityRange[0].floatValue(),
+ 11f, // cons.qualityRange[1].floatValue()
+ AlignmentAnnotation.BAR_GRAPH);
+ if (showConservation)
+ {
+ alignment.addAnnotation(conservation);
+ }
+ quality = new AlignmentAnnotation("Quality",
+ "Alignment Quality based on Blosum62 scores",
+ qannotations,
+ cons.qualityRange[0].floatValue(),
+ cons.qualityRange[1].floatValue(),
+ AlignmentAnnotation.BAR_GRAPH);
+ if (showQuality)
+ {
+ alignment.addAnnotation(quality);
+ }
+ }
+ else
+ {
+ conservation.annotations = annotations;
+ quality.annotations = qannotations;
+ quality.graphMax = cons.qualityRange[1].floatValue();
+ }
+
+ }
+
+ public void updateConsensus()
+ {
+ // this routine prevents vconsensus becoming a new object each time
+ // consenus is calculated. Important for speed of Blosum62
+ // and PID colouring of alignment
+ int aWidth = alignment.getWidth();
+
+ Annotation[] annotations = new Annotation[aWidth];
+
+ hconsensus = new Hashtable[aWidth];
+ AAFrequency.calculate(alignment.getSequencesArray(),
+ 0, aWidth,
+ hconsensus);
+
+ for (int i = 0; i < aWidth; i++)
+ {
+ float value = 0;
+ if(ignoreGapsInConsensusCalculation)
+ value = ((Float)hconsensus[i].get("pid_nogaps")).floatValue();
+ else
+ value = ((Float)hconsensus[i].get("pid_gaps")).floatValue();
+
+ String maxRes = hconsensus[i].get("maxResidue").toString();
+ String mouseOver = hconsensus[i].get("maxResidue") + " ";
+ if (maxRes.length() > 1)
+ {
+ mouseOver = "[" + maxRes + "] ";
+ maxRes = "+";
+ }
+
+
+ mouseOver += (int) value + "%";
+ annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);
+
+ }
+
+ if (consensus == null)
+ {
+ consensus = new AlignmentAnnotation("Consensus",
+ "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ if (showConsensus)
+ {
+ alignment.addAnnotation(consensus);
+ }
+ }
+ else
+ {
+ consensus.annotations = annotations;
+ }
+
+ if(globalColourScheme!=null)
+ globalColourScheme.setConsensus(hconsensus);
+
+ }
+ /**
+ * get the consensus sequence as displayed under the PID consensus annotation row.
+ * @return consensus sequence as a new sequence object
+ */
+ /**
+ * get the consensus sequence as displayed under the PID consensus annotation row.
+ * @return consensus sequence as a new sequence object
+ */
+ public SequenceI getConsensusSeq() {
+ if (consensus==null)
+ updateConsensus();
+ if (consensus==null)
+ return null;
+ StringBuffer seqs=new StringBuffer();
+ for (int i=0; i<consensus.annotations.length; i++) {
+ if (consensus.annotations[i]!=null) {
+ if (consensus.annotations[i].description.charAt(0) == '[')
+ seqs.append(consensus.annotations[i].description.charAt(1));
+ else
+ seqs.append(consensus.annotations[i].displayCharacter);
+ }
+ }
+ SequenceI sq = new Sequence("Consensus", seqs.toString());
+ sq.setDescription("Percentage Identity Consensus "+((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
+ return sq;
+ }
+ public SequenceGroup getSelectionGroup()
+ {
+ return selectionGroup;
+ }
+
+ public void setSelectionGroup(SequenceGroup sg)
+ {
+ selectionGroup = sg;
+ }
+
+ public boolean getConservationSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ public void setConservationSelected(boolean b)
+ {
+ conservationColourSelected = b;
+ }
+
+ public boolean getAbovePIDThreshold()
+ {
+ return abovePIDThreshold;
+ }
+
+ public void setAbovePIDThreshold(boolean b)
+ {
+ abovePIDThreshold = b;
+ }
+
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ public int getStartSeq()
+ {
+ return startSeq;
+ }
+
+ public void setGlobalColourScheme(ColourSchemeI cs)
+ {
+ globalColourScheme = cs;
+ }
+
+ public ColourSchemeI getGlobalColourScheme()
+ {
+ return globalColourScheme;
+ }
+
+ public void setStartRes(int res)
+ {
+ this.startRes = res;
+ }
+
+ public void setStartSeq(int seq)
+ {
+ this.startSeq = seq;
+ }
+
+ public void setEndRes(int res)
+ {
+ if (res > alignment.getWidth() - 1)
+ {
+ // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));
+ res = alignment.getWidth() - 1;
+ }
+ if (res < 0)
+ {
+ res = 0;
+ }
+ this.endRes = res;
+ }
+
+ public void setEndSeq(int seq)
+ {
+ if (seq > alignment.getHeight())
+ {
+ seq = alignment.getHeight();
+ }
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+ this.endSeq = seq;
+ }
+
+ public int getEndSeq()
+ {
+ return endSeq;
+ }
+
+ java.awt.Frame nullFrame;
+ public void setFont(Font f)
+ {
+ font = f;
+ if(nullFrame == null)
+ {
+ nullFrame = new java.awt.Frame();
+ nullFrame.addNotify();
+ }
+
+ java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
+ setCharHeight(fm.getHeight());
+ charWidth = fm.charWidth('M');
+
+ if(upperCasebold)
+ {
+ Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
+ fm = nullFrame.getGraphics().getFontMetrics(f2);
+ charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;
+ }
+ }
+
+ public Font getFont()
+ {
+ return font;
+ }
+
+ public int getCharWidth()
+ {
+ return charWidth;
+ }
+
+ public void setCharHeight(int h)
+ {
+ this.charHeight = h;
+ }
+
+ public int getCharHeight()
+ {
+ return charHeight;
+ }
+
+ public void setWrappedWidth(int w)
+ {
+ this.wrappedWidth = w;
+ }
+
+ public int getwrappedWidth()
+ {
+ return wrappedWidth;
+ }
+
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ public void setAlignment(AlignmentI align)
+ {
+ this.alignment = align;
+ }
+
+ public void setWrapAlignment(boolean state)
+ {
+ wrapAlignment = state;
+ }
+
+ public void setShowText(boolean state)
+ {
+ showText = state;
+ }
+
+ public void setRenderGaps(boolean state)
+ {
+ renderGaps = state;
+ }
+
+ public boolean getColourText()
+ {
+ return showColourText;
+ }
+
+ public void setColourText(boolean state)
+ {
+ showColourText = state;
+ }
+
+ public void setShowBoxes(boolean state)
+ {
+ showBoxes = state;
+ }
+
+ public boolean getWrapAlignment()
+ {
+ return wrapAlignment;
+ }
+
+ public boolean getShowText()
+ {
+ return showText;
+ }
+
+ public boolean getShowBoxes()
+ {
+ return showBoxes;
+ }
+
+ public char getGapCharacter()
+ {
+ return getAlignment().getGapCharacter();
+ }
+
+ public void setGapCharacter(char gap)
+ {
+ if (getAlignment() != null)
+ {
+ getAlignment().setGapCharacter(gap);
+ }
+ }
+
+ public void setThreshold(int thresh)
+ {
+ threshold = thresh;
+ }
+
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setIncrement(int inc)
+ {
+ increment = inc;
+ }
+
+ public int getIncrement()
+ {
+ return increment;
+ }
+
+ public void setHiddenColumns(ColumnSelection colsel)
+ {
+ this.colSel = colsel;
+ if(colSel.getHiddenColumns()!=null)
+ hasHiddenColumns = true;
+ }
+
+ public ColumnSelection getColumnSelection()
+ {
+ return colSel;
+ }
+
+ public void resetSeqLimits(int height)
+ {
+ setEndSeq(height / getCharHeight());
+ }
+
+ public void setCurrentTree(NJTree tree)
+ {
+ currentTree = tree;
+ }
+
+ public NJTree getCurrentTree()
+ {
+ return currentTree;
+ }
+
+ public void setColourAppliesToAllGroups(boolean b)
+ {
+ colourAppliesToAllGroups = b;
+ }
+
+ public boolean getColourAppliesToAllGroups()
+ {
+ return colourAppliesToAllGroups;
+ }
+
+ public boolean getShowJVSuffix()
+ {
+ return showJVSuffix;
+ }
+
+ public void setShowJVSuffix(boolean b)
+ {
+ showJVSuffix = b;
+ }
+
+ public boolean getShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ public void setShowAnnotation(boolean b)
+ {
+ showAnnotation = b;
+ }
+
+ public boolean getScaleAboveWrapped()
+ {
+ return scaleAboveWrapped;
+ }
+
+ public boolean getScaleLeftWrapped()
+ {
+ return scaleLeftWrapped;
+ }
+
+ public boolean getScaleRightWrapped()
+ {
+ return scaleRightWrapped;
+ }
+
+ public void setScaleAboveWrapped(boolean b)
+ {
+ scaleAboveWrapped = b;
+ }
+
+ public void setScaleLeftWrapped(boolean b)
+ {
+ scaleLeftWrapped = b;
+ }
+
+ public void setScaleRightWrapped(boolean b)
+ {
+ scaleRightWrapped = b;
+ }
+
+ public void setIgnoreGapsConsensus(boolean b)
+ {
+ ignoreGapsInConsensusCalculation = b;
+ updateConsensus();
+ if (globalColourScheme!=null)
+ {
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ ignoreGapsInConsensusCalculation);
+
+ }
+ }
+
+ /**
+ * Property change listener for changes in alignment
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public void addPropertyChangeListener(
+ java.beans.PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public void removePropertyChangeListener(
+ java.beans.PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+
+ /**
+ * Property change listener for changes in alignment
+ *
+ * @param prop DOCUMENT ME!
+ * @param oldvalue DOCUMENT ME!
+ * @param newvalue DOCUMENT ME!
+ */
+ public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+ {
+ changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+ }
+
+
+
+ public boolean getIgnoreGapsConsensus()
+ {
+ return ignoreGapsInConsensusCalculation;
+ }
+ public void hideSelectedColumns()
+ {
+ if (colSel.size() < 1)
+ return;
+
+ colSel.hideSelectedColumns();
+ setSelectionGroup(null);
+
+ hasHiddenColumns = true;
+ }
+
+ public void invertColumnSelection()
+ {
+ int column;
+ for (int i = 0; i < alignment.getWidth(); i++)
+ {
+ column = i;
+
+ if (colSel.contains(column))
+ colSel.removeElement(column);
+ else
+ colSel.addElement(column);
+
+ }
+ }
+
+
+ public void hideColumns(int start, int end)
+ {
+ if(start==end)
+ colSel.hideColumns(start);
+ else
+ colSel.hideColumns(start, end);
+
+ hasHiddenColumns = true;
+ }
+
+ public void hideAllSelectedSeqs()
+ {
+ if (selectionGroup == null)
+ return;
+
+ SequenceI[] seqs = selectionGroup.getSequencesInOrder(alignment);
+
+ hideSequence(seqs);
+
+ setSelectionGroup(null);
+ }
+
+ public void hideSequence(SequenceI [] seq)
+ {
+ if(seq!=null)
+ {
+ for (int i = 0; i < seq.length; i++)
+ alignment.getHiddenSequences().hideSequence(seq[i]);
+
+ hasHiddenRows = true;
+ firePropertyChange("alignment", null, alignment.getSequences());
+ }
+ }
+
+ public void showColumn(int col)
+ {
+ colSel.revealHiddenColumns(col);
+ if(colSel.getHiddenColumns()==null)
+ hasHiddenColumns = false;
+ }
+
+ public void showAllHiddenColumns()
+ {
+ colSel.revealAllHiddenColumns();
+ hasHiddenColumns = false;
+ }
+
+ public void showAllHiddenSeqs()
+ {
+ if(alignment.getHiddenSequences().getSize()>0)
+ {
+ if(selectionGroup==null)
+ {
+ selectionGroup = new SequenceGroup();
+ selectionGroup.setEndRes(alignment.getWidth()-1);
+ }
+ Vector tmp = alignment.getHiddenSequences().showAll();
+ for(int t=0; t<tmp.size(); t++)
+ {
+ selectionGroup.addSequence(
+ (SequenceI)tmp.elementAt(t), false
+ );
+ }
+ firePropertyChange("alignment", null, alignment.getSequences());
+ hasHiddenRows = false;
+ }
+ }
+
+ public int adjustForHiddenSeqs(int alignmentIndex)
+ {
+ return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);
+ }
+
+ /**
+ * This method returns the a new SequenceI [] with
+ * the selection sequence and start and end points adjusted
+ * @return String[]
+ */
+ public SequenceI[] getSelectionAsNewSequence()
+ {
+ SequenceI[] sequences;
+
+ if (selectionGroup == null)
+ sequences = alignment.getSequencesArray();
+ else
+ sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+
+ return sequences;
+ }
+
+ /**
+ * This method returns the visible alignment as text, as
+ * seen on the GUI, ie if columns are hidden they will not
+ * be returned in the result.
+ * Use this for calculating trees, PCA, redundancy etc on views
+ * which contain hidden columns.
+ * @return String[]
+ */
+ public jalview.datamodel.CigarArray getViewAsCigars(boolean selectedRegionOnly)
+ {
+ CigarArray selection=null;
+ SequenceI [] seqs= null;
+ int i, iSize;
+ int start = 0, end = 0;
+ if(selectedRegionOnly && selectionGroup!=null)
+ {
+ iSize = selectionGroup.getSize(false);
+ seqs = selectionGroup.getSequencesInOrder(alignment);
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+ }
+ else
+ {
+ iSize = alignment.getHeight();
+ seqs = alignment.getSequencesArray();
+ end = alignment.getWidth()-1;
+ }
+ SeqCigar[] selseqs = new SeqCigar[iSize];
+ for(i=0; i<iSize; i++)
+ {
+ selseqs[i] = new SeqCigar(seqs[i], start, end);
+ }
+ selection=new CigarArray(selseqs);
+ // now construct the CigarArray operations
+ if (hasHiddenColumns) {
+ Vector regions = colSel.getHiddenColumns();
+ int [] region;
+ int hideStart, hideEnd;
+ int last=start;
+ for (int j = 0; last<end & j < regions.size(); j++)
+ {
+ region = (int[]) regions.elementAt(j);
+ hideStart = region[0];
+ hideEnd = region[1];
+ // edit hidden regions to selection range
+ if(hideStart<last) {
+ if (hideEnd > last)
+ {
+ hideStart = last;
+ } else
+ continue;
+ }
+
+ if (hideStart>end)
+ break;
+
+ if (hideEnd>end)
+ hideEnd=end;
+
+ if (hideStart>hideEnd)
+ break;
+ /**
+ * form operations...
+ */
+ if (last<hideStart)
+ selection.addOperation(CigarArray.M, hideStart-last);
+ selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
+ last = hideEnd+1;
+ }
+ // Final match if necessary.
+ if (last<end)
+ selection.addOperation(CigarArray.M, end-last+1);
+ } else {
+ selection.addOperation(CigarArray.M, end-start+1);
+ }
+ return selection;
+ }
+ /**
+ * return a compact representation of the current alignment selection to
+ * pass to an analysis function
+ * @param selectedOnly boolean true to just return the selected view
+ * @return AlignmentView
+ */
+ jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly) {
+ // JBPNote:
+ // this is here because the AlignmentView constructor modifies the CigarArray
+ // object. Refactoring of Cigar and alignment view representation should
+ // be done to remove redundancy.
+ CigarArray aligview = getViewAsCigars(selectedOnly);
+ if (aligview!=null) {
+ return new AlignmentView(aligview,
+ (selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
+ }
+ return null;
+ }
+ /**
+ * This method returns the visible alignment as text, as
+ * seen on the GUI, ie if columns are hidden they will not
+ * be returned in the result.
+ * Use this for calculating trees, PCA, redundancy etc on views
+ * which contain hidden columns.
+ * @return String[]
+ */
+ public String [] getViewAsString(boolean selectedRegionOnly)
+ {
+ String [] selection = null;
+ SequenceI [] seqs= null;
+ int i, iSize;
+ int start = 0, end = 0;
+ if(selectedRegionOnly && selectionGroup!=null)
+ {
+ iSize = selectionGroup.getSize(false);
+ seqs = selectionGroup.getSequencesInOrder(alignment);
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes()+1;
+ }
+ else
+ {
+ iSize = alignment.getHeight();
+ seqs = alignment.getSequencesArray();
+ end = alignment.getWidth();
+ }
+
+ selection = new String[iSize];
+
+
+ for(i=0; i<iSize; i++)
+ {
+ if (hasHiddenColumns)
+ {
+ StringBuffer visibleSeq = new StringBuffer();
+ Vector regions = colSel.getHiddenColumns();
+
+ int blockStart = start, blockEnd=end;
+ int [] region;
+ int hideStart, hideEnd;
+
+ for (int j = 0; j < regions.size(); j++)
+ {
+ region = (int[]) regions.elementAt(j);
+ hideStart = region[0];
+ hideEnd = region[1];
+
+ if(hideStart < start)
+ {
+ continue;
+ }
+
+ blockStart = Math.min(blockStart, hideEnd+1);
+ blockEnd = Math.min(blockEnd, hideStart);
+
+ if(blockStart>blockEnd)
+ {
+ break;
+ }
+
+
+ visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
+
+ blockStart = hideEnd+1;
+ blockEnd = end;
+ }
+
+ if(end>blockStart)
+ visibleSeq.append(seqs[i].getSequence(blockStart, end));
+
+ selection[i] = visibleSeq.toString();
+ }
+ else
+ {
+ selection[i] = seqs[i].getSequence(start, end);
+ }
+ }
+
+ return selection;
+ }
+
+ public boolean getShowHiddenMarkers()
+ {
+ return showHiddenMarkers;
+ }
+
+ public void setShowHiddenMarkers(boolean show)
+ {
+ showHiddenMarkers = show;
+ }
+
+
+}
git://source.jalview.org / jalview.git / commitdiff