- /*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 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
-package jalview.gui;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.bin.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class AlignViewport\r
-{\r
- int startRes;\r
- int endRes;\r
- int startSeq;\r
- int endSeq;\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 showIdentity = true;\r
- boolean colourAppliesToAllGroups = true;\r
- ColourSchemeI globalColourScheme = null;\r
- boolean conservationColourSelected = false;\r
- boolean abovePIDThreshold = false;\r
- SequenceGroup selectionGroup;\r
- int charHeight;\r
- int charWidth;\r
- boolean validCharWidth;\r
- int wrappedWidth;\r
- Font font;\r
- AlignmentI alignment;\r
- ColumnSelection colSel = new ColumnSelection();\r
- int threshold;\r
- int increment;\r
- NJTree currentTree = null;\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
- // JBPNote Prolly only need this in the applet version.\r
- private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);\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
- * @param al DOCUMENT ME!\r
- */\r
- public AlignViewport(AlignmentI al)\r
- {\r
- setAlignment(al);\r
- init();\r
- }\r
- /**\r
- * Create a new AlignViewport with hidden regions\r
- * @param al AlignmentI\r
- * @param hiddenColumns ColumnSelection\r
- */\r
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) {\r
- setAlignment(al);\r
- if (hiddenColumns!=null) {\r
- this.colSel = hiddenColumns;\r
- if (hiddenColumns.getHiddenColumns() != null)\r
- hasHiddenColumns = true;\r
- }\r
- init();\r
- }\r
-\r
- void init()\r
- {\r
- this.startRes = 0;\r
- this.endRes = alignment.getWidth() - 1;\r
- this.startSeq = 0;\r
- this.endSeq = alignment.getHeight() - 1;\r
-\r
- antiAlias = Cache.getDefault("ANTI_ALIAS", false);\r
-\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
- int style = 0;\r
-\r
- if (fontStyle.equals("bold"))\r
- {\r
- style = 1;\r
- }\r
- else if (fontStyle.equals("italic"))\r
- {\r
- style = 2;\r
- }\r
-\r
- setFont(new Font(fontName, style, Integer.parseInt(fontSize)));\r
-\r
-\r
- alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );\r
-\r
-\r
- // We must set conservation and consensus before setting colour,\r
- // as Blosum and Clustal require this to be done\r
- if(vconsensus==null && !isDataset)\r
- {\r
- updateConservation();\r
- updateConsensus();\r
- }\r
-\r
- if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)\r
- {\r
- globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
- jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));\r
-\r
- if (globalColourScheme instanceof UserColourScheme)\r
- {\r
- globalColourScheme = UserDefinedColours.loadDefaultColours();\r
- ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());\r
- }\r
-\r
- if (globalColourScheme != null)\r
- {\r
- globalColourScheme.setConsensus(vconsensus);\r
- }\r
- }\r
- }\r
-\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\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
- alignment.getSequences(), 0, alignment.getWidth() - 1);\r
- cons.calculate();\r
- cons.verdict(false, ConsPercGaps);\r
- cons.findQuality();\r
-\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;\r
- float minG;\r
- float minB;\r
- float maxR;\r
- float maxG;\r
- float 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
-\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
-\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
-\r
- if (sequence.charAt(i) == '+')\r
- {\r
- value = 10;\r
- }\r
- }\r
-\r
- float vprop = value - min;\r
- vprop /= max;\r
- annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- String.valueOf(value), ' ', value,\r
- new Color(minR + (maxR * vprop),\r
- minG + (maxG * vprop),\r
- minB + (maxB * vprop)));\r
-\r
- // Quality calc\r
- value = ( (Double) cons.quality.get(i)).floatValue();\r
- vprop = value - qmin;\r
- vprop /= qmax;\r
- qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',\r
- value,\r
- new 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, 0f, // cons.qualityRange[0].floatValue(),\r
- 11f, // cons.qualityRange[1].floatValue()\r
- AlignmentAnnotation.BAR_GRAPH);\r
-\r
- if (showConservation)\r
- {\r
- alignment.addAnnotation(conservation);\r
- }\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
-\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
- catch (OutOfMemoryError error)\r
- {\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
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateConsensus()\r
- {\r
- try{\r
- Annotation[] annotations = new Annotation[alignment.getWidth()];\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
- if (vconsensus == null)\r
- {\r
- vconsensus = alignment.getAAFrequency();\r
- }\r
- else\r
- {\r
- Vector temp = alignment.getAAFrequency();\r
- vconsensus.clear();\r
-\r
- Enumeration e = temp.elements();\r
-\r
- while (e.hasMoreElements())\r
- {\r
- vconsensus.add(e.nextElement());\r
- }\r
- }\r
-\r
- Hashtable hash = null;\r
-\r
- for (int i = 0; i < alignment.getWidth(); i++)\r
- {\r
- hash = (Hashtable) vconsensus.elementAt(i);\r
-\r
- float value = 0;\r
- if (ignoreGapsInConsensusCalculation)\r
- value = ( (Float) hash.get("pid_nogaps")).floatValue();\r
- else\r
- value = ( (Float) hash.get("pid_gaps")).floatValue();\r
-\r
- String maxRes = hash.get("maxResidue").toString();\r
- String mouseOver = hash.get("maxResidue") + " ";\r
-\r
- if (maxRes.length() > 1)\r
- {\r
- mouseOver = "[" + maxRes + "] ";\r
- maxRes = "+";\r
- }\r
-\r
- mouseOver += ( (int) value + "%");\r
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
- }\r
-\r
- if (consensus == null)\r
- {\r
- consensus = new AlignmentAnnotation("Consensus", "PID",\r
- annotations, 0f, 100f,AlignmentAnnotation.BAR_GRAPH);\r
-\r
- if (showIdentity)\r
- {\r
- alignment.addAnnotation(consensus);\r
- }\r
- }\r
- else\r
- {\r
- consensus.annotations = annotations;\r
- }\r
-\r
- if (globalColourScheme != null)\r
- globalColourScheme.setConsensus(vconsensus);\r
-\r
- }catch(OutOfMemoryError error)\r
- {\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
-\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceGroup getSelectionGroup()\r
- {\r
- return selectionGroup;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param sg DOCUMENT ME!\r
- */\r
- public void setSelectionGroup(SequenceGroup sg)\r
- {\r
- selectionGroup = sg;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getConservationSelected()\r
- {\r
- return conservationColourSelected;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void setConservationSelected(boolean b)\r
- {\r
- conservationColourSelected = b;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getAbovePIDThreshold()\r
- {\r
- return abovePIDThreshold;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void setAbovePIDThreshold(boolean b)\r
- {\r
- abovePIDThreshold = b;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getStartRes()\r
- {\r
- return startRes;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getEndRes()\r
- {\r
- return endRes;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getStartSeq()\r
- {\r
- return startSeq;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param cs DOCUMENT ME!\r
- */\r
- public void setGlobalColourScheme(ColourSchemeI cs)\r
- {\r
- globalColourScheme = cs;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public ColourSchemeI getGlobalColourScheme()\r
- {\r
- return globalColourScheme;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param res DOCUMENT ME!\r
- */\r
- public void setStartRes(int res)\r
- {\r
- this.startRes = res;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq DOCUMENT ME!\r
- */\r
- public void setStartSeq(int seq)\r
- {\r
- this.startSeq = seq;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param res DOCUMENT ME!\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
-\r
- if (res < 0)\r
- {\r
- res = 0;\r
- }\r
-\r
- this.endRes = res;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq DOCUMENT ME!\r
- */\r
- public void setEndSeq(int seq)\r
- {\r
- if (seq > alignment.getHeight())\r
- {\r
- seq = alignment.getHeight();\r
- }\r
-\r
- if (seq < 0)\r
- {\r
- seq = 0;\r
- }\r
-\r
- this.endSeq = seq;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getEndSeq()\r
- {\r
- return endSeq;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param f DOCUMENT ME!\r
- */\r
- public void setFont(Font f)\r
- {\r
- font = f;\r
-\r
- Container c = new Container();\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
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Font getFont()\r
- {\r
- return font;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param w DOCUMENT ME!\r
- */\r
- public void setCharWidth(int w)\r
- {\r
- this.charWidth = w;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getCharWidth()\r
- {\r
- return charWidth;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param h DOCUMENT ME!\r
- */\r
- public void setCharHeight(int h)\r
- {\r
- this.charHeight = h;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getCharHeight()\r
- {\r
- return charHeight;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param w DOCUMENT ME!\r
- */\r
- public void setWrappedWidth(int w)\r
- {\r
- this.wrappedWidth = w;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getWrappedWidth()\r
- {\r
- return wrappedWidth;\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public AlignmentI getAlignment()\r
- {\r
- return alignment;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param align DOCUMENT ME!\r
- */\r
- public void setAlignment(AlignmentI align)\r
- {\r
- this.alignment = align;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param state DOCUMENT ME!\r
- */\r
- public void setWrapAlignment(boolean state)\r
- {\r
- wrapAlignment = state;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param state DOCUMENT ME!\r
- */\r
- public void setShowText(boolean state)\r
- {\r
- showText = state;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param state DOCUMENT ME!\r
- */\r
- public void setRenderGaps(boolean state)\r
- {\r
- renderGaps = state;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getColourText()\r
- {\r
- return showColourText;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param state DOCUMENT ME!\r
- */\r
- public void setColourText(boolean state)\r
- {\r
- showColourText = state;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param state DOCUMENT ME!\r
- */\r
- public void setShowBoxes(boolean state)\r
- {\r
- showBoxes = state;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getWrapAlignment()\r
- {\r
- return wrapAlignment;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getShowText()\r
- {\r
- return showText;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getShowBoxes()\r
- {\r
- return showBoxes;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public char getGapCharacter()\r
- {\r
- return getAlignment().getGapCharacter();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param gap DOCUMENT ME!\r
- */\r
- public void setGapCharacter(char gap)\r
- {\r
- if (getAlignment() != null)\r
- {\r
- getAlignment().setGapCharacter(gap);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param thresh DOCUMENT ME!\r
- */\r
- public void setThreshold(int thresh)\r
- {\r
- threshold = thresh;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getThreshold()\r
- {\r
- return threshold;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param inc DOCUMENT ME!\r
- */\r
- public void setIncrement(int inc)\r
- {\r
- increment = inc;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getIncrement()\r
- {\r
- return increment;\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public ColumnSelection getColumnSelection()\r
- {\r
- return colSel;\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param tree DOCUMENT ME!\r
- */\r
- public void setCurrentTree(NJTree tree)\r
- {\r
- currentTree = tree;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public NJTree getCurrentTree()\r
- {\r
- return currentTree;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void setColourAppliesToAllGroups(boolean b)\r
- {\r
- colourAppliesToAllGroups = b;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getColourAppliesToAllGroups()\r
- {\r
- return colourAppliesToAllGroups;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getShowJVSuffix()\r
- {\r
- return showJVSuffix;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void setShowJVSuffix(boolean b)\r
- {\r
- showJVSuffix = b;\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getShowAnnotation()\r
- {\r
- return showAnnotation;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void setShowAnnotation(boolean b)\r
- {\r
- showAnnotation = b;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getScaleAboveWrapped()\r
- {\r
- return scaleAboveWrapped;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getScaleLeftWrapped()\r
- {\r
- return scaleLeftWrapped;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean getScaleRightWrapped()\r
- {\r
- return scaleRightWrapped;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void setScaleAboveWrapped(boolean b)\r
- {\r
- scaleAboveWrapped = b;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void setScaleLeftWrapped(boolean b)\r
- {\r
- scaleLeftWrapped = b;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void setScaleRightWrapped(boolean b)\r
- {\r
- scaleRightWrapped = b;\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
- public void setIgnoreGapsConsensus(boolean b)\r
- {\r
- ignoreGapsInConsensusCalculation = b;\r
- updateConsensus();\r
- if(globalColourScheme!=null)\r
- {\r
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);\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.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
- Vector tmp = alignment.getHiddenSequences().showSequence(index);\r
- if(tmp.size()>0)\r
- {\r
- if(selectionGroup==null)\r
- {\r
- selectionGroup = new SequenceGroup();\r
- selectionGroup.setEndRes(alignment.getWidth()-1);\r
- }\r
-\r
- for (int t = 0; t < tmp.size(); t++)\r
- {\r
- selectionGroup.addSequence(\r
- (SequenceI) tmp.elementAt(t), false\r
- );\r
- }\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
- 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
- hasHiddenRows = false;\r
- }\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 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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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.gui;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.api.StructureSelectionManagerProvider;
+
+import jalview.bin.*;
+
+import jalview.datamodel.*;
+
+import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.141 $
+ */
+public class AlignViewport implements SelectionSource, VamsasSource
+{
+ private static final int RIGHT_JUSTIFY = 1;
+
+ int startRes;
+
+ int endRes;
+
+ int startSeq;
+
+ int endSeq;
+
+ 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 colourAppliesToAllGroups = true;
+
+ ColourSchemeI globalColourScheme = null;
+
+ boolean conservationColourSelected = false;
+
+ boolean abovePIDThreshold = false;
+
+ SequenceGroup selectionGroup;
+
+ int charHeight;
+
+ int charWidth;
+
+ boolean validCharWidth;
+
+ int wrappedWidth;
+
+ Font font;
+
+ boolean seqNameItalics;
+
+ AlignmentI alignment;
+
+ ColumnSelection colSel = new ColumnSelection();
+
+ int threshold;
+
+ int increment;
+
+ NJTree currentTree = null;
+
+ boolean scaleAboveWrapped = false;
+
+ boolean scaleLeftWrapped = true;
+
+ boolean scaleRightWrapped = true;
+
+ boolean hasHiddenColumns = false;
+
+ boolean hasHiddenRows = false;
+
+ boolean showHiddenMarkers = true;
+
+ boolean cursorMode = false;
+
+ /**
+ * Keys are the feature types which are currently visible. Note: Values are
+ * not used!
+ */
+ Hashtable featuresDisplayed = null;
+
+ /** DOCUMENT ME!! */
+ public Hashtable[] hconsensus;
+
+ public Hashtable[] hStrucConsensus;
+
+ AlignmentAnnotation consensus;
+
+ AlignmentAnnotation strucConsensus;
+
+ AlignmentAnnotation conservation;
+
+ AlignmentAnnotation quality;
+
+ AlignmentAnnotation[] groupConsensus;
+
+ AlignmentAnnotation[] groupConservation;
+
+ boolean autoCalculateConsensus = true;
+
+ boolean autoCalculateStrucConsensus = true;
+
+ /** DOCUMENT ME!! */
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+ // JBPNote Prolly only need this in the applet version.
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(
+ this);
+
+ boolean ignoreGapsInConsensusCalculation = false;
+
+ boolean isDataset = false;
+
+ boolean antiAlias = false;
+
+ boolean padGaps = false;
+
+ Rectangle explodedPosition;
+
+ String viewName;
+
+ String sequenceSetID;
+
+ boolean gatherViewsHere = false;
+
+ Stack historyList = new Stack();
+
+ Stack redoList = new Stack();
+
+ Hashtable sequenceColours;
+
+ int thresholdTextColour = 0;
+
+ Color textColour = Color.black;
+
+ Color textColour2 = Color.white;
+
+ boolean rightAlignIds = false;
+
+ Hashtable hiddenRepSequences;
+
+ boolean sortByTree;
+
+ /**
+ * Creates a new AlignViewport object.
+ *
+ * @param al
+ * alignment to view
+ */
+ public AlignViewport(AlignmentI al)
+ {
+ setAlignment(al);
+ init();
+ }
+
+ /**
+ * Create a new AlignViewport object with a specific sequence set ID
+ *
+ * @param al
+ * @param seqsetid
+ * (may be null - but potential for ambiguous constructor exception)
+ */
+ public AlignViewport(AlignmentI al, String seqsetid)
+ {
+ this(al, seqsetid, null);
+ }
+
+ public AlignViewport(AlignmentI al, String seqsetid, String viewid)
+ {
+ sequenceSetID = seqsetid;
+ viewId = viewid;
+ // TODO remove these once 2.4.VAMSAS release finished
+ if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ {
+ Cache.log.debug("Setting viewport's sequence set id : "
+ + sequenceSetID);
+ }
+ if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ {
+ Cache.log.debug("Setting viewport's view id : " + viewId);
+ }
+ setAlignment(al);
+ init();
+ }
+
+ /**
+ * Create a new AlignViewport with hidden regions
+ *
+ * @param al
+ * AlignmentI
+ * @param hiddenColumns
+ * ColumnSelection
+ */
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+ {
+ setAlignment(al);
+ if (hiddenColumns != null)
+ {
+ this.colSel = hiddenColumns;
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
+ {
+ hasHiddenColumns = true;
+ }
+ else
+ {
+ hasHiddenColumns = false;
+ }
+ }
+ init();
+ }
+
+ /**
+ * New viewport with hidden columns and an existing sequence set id
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param seqsetid
+ * (may be null)
+ */
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ String seqsetid)
+ {
+ this(al, hiddenColumns, seqsetid, null);
+ }
+
+ /**
+ * New viewport with hidden columns and an existing sequence set id and viewid
+ *
+ * @param al
+ * @param hiddenColumns
+ * @param seqsetid
+ * (may be null)
+ * @param viewid
+ * (may be null)
+ */
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ String seqsetid, String viewid)
+ {
+ sequenceSetID = seqsetid;
+ viewId = viewid;
+ // TODO remove these once 2.4.VAMSAS release finished
+ if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ {
+ Cache.log.debug("Setting viewport's sequence set id : "
+ + sequenceSetID);
+ }
+ if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ {
+ Cache.log.debug("Setting viewport's view id : " + viewId);
+ }
+ setAlignment(al);
+ if (hiddenColumns != null)
+ {
+ this.colSel = hiddenColumns;
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
+ {
+ hasHiddenColumns = true;
+ }
+ else
+ {
+ hasHiddenColumns = false;
+ }
+ }
+ init();
+ }
+
+ void init()
+ {
+ this.startRes = 0;
+ this.endRes = alignment.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = alignment.getHeight() - 1;
+
+ antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+
+ showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
+ showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+
+ rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+ centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+ padGaps = Cache.getDefault("PAD_GAPS", true);
+ shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
+ showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
+
+ String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+ String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+ String fontSize = Cache.getDefault("FONT_SIZE", "10");
+
+ seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+
+ int style = 0;
+
+ if (fontStyle.equals("bold"))
+ {
+ style = 1;
+ }
+ else if (fontStyle.equals("italic"))
+ {
+ style = 2;
+ }
+
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+
+ alignment
+ .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+
+ // We must set conservation and consensus before setting colour,
+ // as Blosum and Clustal require this to be done
+ if (hconsensus == null && !isDataset)
+ {
+ if (!alignment.isNucleotide())
+ {
+ conservation = new AlignmentAnnotation("Conservation",
+ "Conservation of total alignment less than " + ConsPercGaps
+ + "% gaps", new Annotation[1], 0f, 11f,
+ AlignmentAnnotation.BAR_GRAPH);
+ conservation.hasText = true;
+ conservation.autoCalculated = true;
+
+ if (Cache.getDefault("SHOW_CONSERVATION", true))
+ {
+ alignment.addAnnotation(conservation);
+ }
+
+ if (Cache.getDefault("SHOW_QUALITY", true))
+ {
+ quality = new AlignmentAnnotation("Quality",
+ "Alignment Quality based on Blosum62 scores",
+ new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+ quality.hasText = true;
+ quality.autoCalculated = true;
+
+ alignment.addAnnotation(quality);
+ }
+ showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
+ false);
+
+ {
+
+ }
+ }
+ showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
+ true);
+ showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+ showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
+ // TODO: add menu option action that nulls or creates consensus object
+ // depending on if the user wants to see the annotation or not in a
+ // specific alignment
+ consensus = new AlignmentAnnotation("Consensus", "PID",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ consensus.hasText = true;
+ consensus.autoCalculated = true;
+
+ if (alignment.isNucleotide() && alignment.hasRNAStructure())
+ {
+ strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ strucConsensus.hasText = true;
+ strucConsensus.autoCalculated = true;
+ }
+
+ if (Cache.getDefault("SHOW_IDENTITY", true))
+ {
+ alignment.addAnnotation(consensus);
+ // TODO: Make own if for structure
+ if (alignment.isNucleotide() && alignment.hasRNAStructure())
+ {
+ alignment.addAnnotation(strucConsensus);
+ }
+ }
+
+ }
+
+ if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+ {
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,
+ jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
+
+ if (globalColourScheme instanceof UserColourScheme)
+ {
+ globalColourScheme = UserDefinedColours.loadDefaultColours();
+ ((UserColourScheme) globalColourScheme).setThreshold(0,
+ getIgnoreGapsConsensus());
+ }
+
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
+ }
+
+ wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
+ showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
+ false);
+ sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
+ followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
+ true);
+ }
+
+ /**
+ * set the flag
+ *
+ * @param b
+ * features are displayed if true
+ */
+ public void setShowSequenceFeatures(boolean b)
+ {
+ showSequenceFeatures = b;
+ }
+
+ public boolean getShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+ ConservationThread conservationThread;
+
+ ConsensusThread consensusThread;
+
+ StrucConsensusThread strucConsensusThread;
+
+ boolean consUpdateNeeded = false;
+
+ static boolean UPDATING_CONSENSUS = false;
+
+ static boolean UPDATING_STRUC_CONSENSUS = false;
+
+ static boolean UPDATING_CONSERVATION = false;
+
+ boolean updatingConsensus = false;
+
+ boolean updatingStrucConsensus = false;
+
+ boolean updatingConservation = false;
+
+ /**
+ * centre columnar annotation labels in displayed alignment annotation TODO:
+ * add to jalviewXML and annotation display settings
+ */
+ boolean centreColumnLabels = false;
+
+ private boolean showdbrefs;
+
+ private boolean shownpfeats;
+
+ /**
+ * trigger update of conservation annotation
+ */
+ public void updateConservation(final AlignmentPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (alignment.isNucleotide() || conservation == null
+ || !autoCalculateConsensus)
+ {
+ return;
+ }
+
+ conservationThread = new ConservationThread(this, ap);
+ conservationThread.start();
+ }
+
+ /**
+ * trigger update of consensus annotation
+ */
+ public void updateConsensus(final AlignmentPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (consensus == null || !autoCalculateConsensus)
+ {
+ return;
+ }
+ consensusThread = new ConsensusThread(ap);
+ consensusThread.start();
+ }
+
+ class ConsensusThread extends Thread
+ {
+ AlignmentPanel ap;
+
+ public ConsensusThread(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ public void run()
+ {
+ updatingConsensus = true;
+ while (UPDATING_CONSENSUS)
+ {
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+
+ Thread.sleep(200);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ UPDATING_CONSENSUS = true;
+
+ try
+ {
+ int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
+ // pointer
+ // possibility
+ // here.
+ if (aWidth <= 0)
+ {
+ updatingConsensus = false;
+ UPDATING_CONSENSUS = false;
+ return;
+ }
+
+ consensus.annotations = null;
+ consensus.annotations = new Annotation[aWidth];
+
+ hconsensus = new Hashtable[aWidth];
+ AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
+ .getWidth(), hconsensus, true);
+ updateAnnotation(true);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
+
+ } catch (OutOfMemoryError error)
+ {
+ alignment.deleteAnnotation(consensus);
+
+ consensus = null;
+ hconsensus = null;
+ new OOMWarning("calculating consensus", error);
+ }
+ UPDATING_CONSENSUS = false;
+ updatingConsensus = false;
+
+ if (ap != null)
+ {
+ ap.paintAlignment(true);
+ }
+ }
+
+ /**
+ * update the consensus annotation from the sequence profile data using
+ * current visualization settings.
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false);
+ }
+
+ protected void updateAnnotation(boolean immediate)
+ {
+ // TODO: make calls thread-safe, so if another thread calls this method,
+ // it will either return or wait until one calculation is finished.
+ if (immediate
+ || (!updatingConsensus && consensus != null && hconsensus != null))
+ {
+ AAFrequency.completeConsensus(consensus, hconsensus, 0,
+ hconsensus.length, ignoreGapsInConsensusCalculation,
+ showSequenceLogo);
+ }
+ }
+ }
+
+ // --------START Structure Conservation
+ public void updateStrucConsensus(final AlignmentPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (strucConsensus == null || !autoCalculateStrucConsensus)
+ {
+ return;
+ }
+ strucConsensusThread = new StrucConsensusThread(ap);
+ strucConsensusThread.start();
+ }
+
+ class StrucConsensusThread extends Thread
+ {
+ AlignmentPanel ap;
+
+ public StrucConsensusThread(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ public void run()
+ {
+ updatingStrucConsensus = true;
+ while (UPDATING_STRUC_CONSENSUS)
+ {
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+
+ Thread.sleep(200);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ UPDATING_STRUC_CONSENSUS = true;
+
+ try
+ {
+ int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
+ // pointer
+ // possibility
+ // here.
+ if (aWidth <= 0)
+ {
+ updatingStrucConsensus = false;
+ UPDATING_STRUC_CONSENSUS = false;
+ return;
+ }
+
+ strucConsensus.annotations = null;
+ strucConsensus.annotations = new Annotation[aWidth];
+
+ hStrucConsensus = new Hashtable[aWidth];
+
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ AlignmentAnnotation rnaStruc = null;
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].getRNAStruc() != null)
+ {
+ rnaStruc = aa[i];
+ break;
+ }
+ }
+
+ AlignmentAnnotation rna = ap.av.getAlignment()
+ .getAlignmentAnnotation()[0];
+ StructureFrequency.calculate(alignment.getSequencesArray(), 0,
+ alignment.getWidth(), hStrucConsensus, true, rnaStruc);
+ // TODO AlignmentAnnotation rnaStruc!!!
+ updateAnnotation(true);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hStrucConsensus);
+ }
+
+ } catch (OutOfMemoryError error)
+ {
+ alignment.deleteAnnotation(strucConsensus);
+
+ strucConsensus = null;
+ hStrucConsensus = null;
+ new OOMWarning("calculating structure consensus", error);
+ }
+ UPDATING_STRUC_CONSENSUS = false;
+ updatingStrucConsensus = false;
+
+ if (ap != null)
+ {
+ ap.paintAlignment(true);
+ }
+ }
+
+ /**
+ * update the consensus annotation from the sequence profile data using
+ * current visualization settings.
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false);
+ }
+
+ protected void updateAnnotation(boolean immediate)
+ {
+ // TODO: make calls thread-safe, so if another thread calls this method,
+ // it will either return or wait until one calculation is finished.
+ if (immediate
+ || (!updatingStrucConsensus && strucConsensus != null && hStrucConsensus != null))
+ {
+ StructureFrequency.completeConsensus(strucConsensus,
+ hStrucConsensus, 0, hStrucConsensus.length, false,
+ showSequenceLogo);
+ }
+ }
+ }
+
+ // --------END Structure Conservation
+
+ /**
+ * 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(null);
+ }
+ 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;
+ }
+
+ /**
+ *
+ *
+ * @return null or the currently selected sequence region
+ */
+ public SequenceGroup getSelectionGroup()
+ {
+ return selectionGroup;
+ }
+
+ /**
+ * Set the selection group for this window.
+ *
+ * @param sg
+ * - group holding references to sequences in this alignment view
+ *
+ */
+ public void setSelectionGroup(SequenceGroup sg)
+ {
+ selectionGroup = sg;
+ }
+
+ /**
+ * GUI state
+ *
+ * @return true if conservation based shading is enabled
+ */
+ public boolean getConservationSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ /**
+ * GUI state
+ *
+ * @param b
+ * enable conservation based shading
+ */
+ public void setConservationSelected(boolean b)
+ {
+ conservationColourSelected = b;
+ }
+
+ /**
+ * GUI state
+ *
+ * @return true if percent identity threshold is applied to shading
+ */
+ public boolean getAbovePIDThreshold()
+ {
+ return abovePIDThreshold;
+ }
+
+ /**
+ * GUI state
+ *
+ *
+ * @param b
+ * indicate if percent identity threshold is applied to shading
+ */
+ public void setAbovePIDThreshold(boolean b)
+ {
+ abovePIDThreshold = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStartSeq()
+ {
+ return startSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cs
+ * DOCUMENT ME!
+ */
+ public void setGlobalColourScheme(ColourSchemeI cs)
+ {
+ globalColourScheme = cs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ColourSchemeI getGlobalColourScheme()
+ {
+ return globalColourScheme;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param res
+ * DOCUMENT ME!
+ */
+ public void setStartRes(int res)
+ {
+ this.startRes = res;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
+ */
+ public void setStartSeq(int seq)
+ {
+ this.startSeq = seq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param res
+ * DOCUMENT ME!
+ */
+ 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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq
+ * DOCUMENT ME!
+ */
+ public void setEndSeq(int seq)
+ {
+ if (seq > alignment.getHeight())
+ {
+ seq = alignment.getHeight();
+ }
+
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+
+ this.endSeq = seq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEndSeq()
+ {
+ return endSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f
+ * DOCUMENT ME!
+ */
+ public void setFont(Font f)
+ {
+ font = f;
+
+ Container c = new Container();
+
+ java.awt.FontMetrics fm = c.getFontMetrics(font);
+ setCharHeight(fm.getHeight());
+ setCharWidth(fm.charWidth('M'));
+ validCharWidth = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont()
+ {
+ return font;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
+ */
+ public void setCharWidth(int w)
+ {
+ this.charWidth = w;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getCharWidth()
+ {
+ return charWidth;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param h
+ * DOCUMENT ME!
+ */
+ public void setCharHeight(int h)
+ {
+ this.charHeight = h;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getCharHeight()
+ {
+ return charHeight;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w
+ * DOCUMENT ME!
+ */
+ public void setWrappedWidth(int w)
+ {
+ this.wrappedWidth = w;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getWrappedWidth()
+ {
+ return wrappedWidth;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align
+ * DOCUMENT ME!
+ */
+ public void setAlignment(AlignmentI align)
+ {
+ if (alignment != null && alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).removeMappings(alignment.getCodonFrames());
+ }
+ this.alignment = align;
+ if (alignment.getCodonFrames() != null)
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).addMappings(alignment.getCodonFrames());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setWrapAlignment(boolean state)
+ {
+ wrapAlignment = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setShowText(boolean state)
+ {
+ showText = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setRenderGaps(boolean state)
+ {
+ renderGaps = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getColourText()
+ {
+ return showColourText;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setColourText(boolean state)
+ {
+ showColourText = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state
+ * DOCUMENT ME!
+ */
+ public void setShowBoxes(boolean state)
+ {
+ showBoxes = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getWrapAlignment()
+ {
+ return wrapAlignment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowText()
+ {
+ return showText;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowBoxes()
+ {
+ return showBoxes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getGapCharacter()
+ {
+ return getAlignment().getGapCharacter();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gap
+ * DOCUMENT ME!
+ */
+ public void setGapCharacter(char gap)
+ {
+ if (getAlignment() != null)
+ {
+ getAlignment().setGapCharacter(gap);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param thresh
+ * DOCUMENT ME!
+ */
+ public void setThreshold(int thresh)
+ {
+ threshold = thresh;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param inc
+ * DOCUMENT ME!
+ */
+ public void setIncrement(int inc)
+ {
+ increment = inc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIncrement()
+ {
+ return increment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ColumnSelection getColumnSelection()
+ {
+ return colSel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tree
+ * DOCUMENT ME!
+ */
+ public void setCurrentTree(NJTree tree)
+ {
+ currentTree = tree;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NJTree getCurrentTree()
+ {
+ return currentTree;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setColourAppliesToAllGroups(boolean b)
+ {
+ colourAppliesToAllGroups = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getColourAppliesToAllGroups()
+ {
+ return colourAppliesToAllGroups;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowJVSuffix()
+ {
+ return showJVSuffix;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setShowJVSuffix(boolean b)
+ {
+ showJVSuffix = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setShowAnnotation(boolean b)
+ {
+ showAnnotation = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleAboveWrapped()
+ {
+ return scaleAboveWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleLeftWrapped()
+ {
+ return scaleLeftWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleRightWrapped()
+ {
+ return scaleRightWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setScaleAboveWrapped(boolean b)
+ {
+ scaleAboveWrapped = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setScaleLeftWrapped(boolean b)
+ {
+ scaleLeftWrapped = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setScaleRightWrapped(boolean b)
+ {
+ scaleRightWrapped = b;
+ }
+
+ /**
+ * 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 void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+ {
+ ignoreGapsInConsensusCalculation = b;
+ updateConsensus(ap);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ ignoreGapsInConsensusCalculation);
+ }
+ }
+
+ public boolean getIgnoreGapsConsensus()
+ {
+ return ignoreGapsInConsensusCalculation;
+ }
+
+ public void setDataset(boolean b)
+ {
+ isDataset = b;
+ }
+
+ public boolean isDataset()
+ {
+ return isDataset;
+ }
+
+ public void hideSelectedColumns()
+ {
+ if (colSel.size() < 1)
+ {
+ return;
+ }
+
+ colSel.hideSelectedColumns();
+ setSelectionGroup(null);
+
+ hasHiddenColumns = true;
+ }
+
+ public void hideColumns(int start, int end)
+ {
+ if (start == end)
+ {
+ colSel.hideColumns(start);
+ }
+ else
+ {
+ colSel.hideColumns(start, end);
+ }
+
+ hasHiddenColumns = true;
+ }
+
+ public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
+ {
+ int sSize = sg.getSize();
+ if (sSize < 2)
+ {
+ return;
+ }
+
+ if (hiddenRepSequences == null)
+ {
+ hiddenRepSequences = new Hashtable();
+ }
+
+ hiddenRepSequences.put(repSequence, sg);
+
+ // Hide all sequences except the repSequence
+ SequenceI[] seqs = new SequenceI[sSize - 1];
+ int index = 0;
+ for (int i = 0; i < sSize; i++)
+ {
+ if (sg.getSequenceAt(i) != repSequence)
+ {
+ if (index == sSize - 1)
+ {
+ return;
+ }
+
+ seqs[index++] = sg.getSequenceAt(i);
+ }
+ }
+ sg.setSeqrep(repSequence);
+ sg.setHidereps(true);
+ hideSequence(seqs);
+
+ }
+
+ public void hideAllSelectedSeqs()
+ {
+ if (selectionGroup == null || selectionGroup.getSize() < 1)
+ {
+ 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 showSequence(int index)
+ {
+ Vector tmp = alignment.getHiddenSequences().showSequence(index,
+ hiddenRepSequences);
+ if (tmp.size() > 0)
+ {
+ if (selectionGroup == null)
+ {
+ selectionGroup = new SequenceGroup();
+ selectionGroup.setEndRes(alignment.getWidth() - 1);
+ }
+
+ for (int t = 0; t < tmp.size(); t++)
+ {
+ selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ }
+ firePropertyChange("alignment", null, alignment.getSequences());
+ sendSelection();
+ }
+
+ if (alignment.getHiddenSequences().getSize() < 1)
+ {
+ hasHiddenRows = false;
+ }
+ }
+
+ 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(
+ hiddenRepSequences);
+ for (int t = 0; t < tmp.size(); t++)
+ {
+ selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ }
+ firePropertyChange("alignment", null, alignment.getSequences());
+ sendSelection();
+ hasHiddenRows = false;
+ hiddenRepSequences = null;
+ }
+ }
+
+ public void invertColumnSelection()
+ {
+ colSel.invertColumnSelection(0, alignment.getWidth());
+ }
+
+ public int adjustForHiddenSeqs(int alignmentIndex)
+ {
+ return alignment.getHiddenSequences().adjustForHiddenSeqs(
+ alignmentIndex);
+ }
+
+ /**
+ * This method returns an array of new SequenceI objects derived from the
+ * whole alignment or just the current selection with start and end points
+ * adjusted
+ *
+ * @note if you need references to the actual SequenceI objects in the
+ * alignment or currently selected then use getSequenceSelection()
+ * @return selection as new sequenceI objects
+ */
+ public SequenceI[] getSelectionAsNewSequence()
+ {
+ SequenceI[] sequences;
+
+ if (selectionGroup == null)
+ {
+ sequences = alignment.getSequencesArray();
+ AlignmentAnnotation[] annots = alignment.getAlignmentAnnotation();
+ for (int i = 0; i < sequences.length; i++)
+ {
+ sequences[i] = new Sequence(sequences[i], annots); // construct new
+ // sequence with
+ // subset of visible
+ // annotation
+ }
+ }
+ else
+ {
+ sequences = selectionGroup.getSelectionAsNewSequences(alignment);
+ }
+
+ return sequences;
+ }
+
+ /**
+ * get the currently selected sequence objects or all the sequences in the
+ * alignment.
+ *
+ * @return array of references to sequence objects
+ */
+ public SequenceI[] getSequenceSelection()
+ {
+ SequenceI[] sequences = null;
+ if (selectionGroup != null)
+ {
+ sequences = selectionGroup.getSequencesInOrder(alignment);
+ }
+ if (sequences == null)
+ {
+ sequences = alignment.getSequencesArray();
+ }
+ 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)
+ {
+ return new jalview.datamodel.CigarArray(alignment,
+ (hasHiddenColumns ? colSel : null),
+ (selectedRegionOnly ? selectionGroup : null));
+ }
+
+ /**
+ * 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
+ */
+ public jalview.datamodel.AlignmentView getAlignmentView(
+ boolean selectedOnly)
+ {
+ return getAlignmentView(selectedOnly, false);
+ }
+
+ /**
+ * 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
+ * @param markGroups
+ * boolean true to annotate the alignment view with groups on the
+ * alignment (and intersecting with selected region if selectedOnly
+ * is true)
+ * @return AlignmentView
+ */
+ public jalview.datamodel.AlignmentView getAlignmentView(
+ boolean selectedOnly, boolean markGroups)
+ {
+ return new AlignmentView(alignment, colSel, selectionGroup,
+ hasHiddenColumns, selectedOnly, markGroups);
+ }
+
+ /**
+ * 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();
+ 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];
+ if (hasHiddenColumns)
+ {
+ selection = colSel.getVisibleSequenceStrings(start, end, seqs);
+ }
+ else
+ {
+ for (i = 0; i < iSize; i++)
+ {
+ selection[i] = seqs[i].getSequenceAsString(start, end);
+ }
+
+ }
+ return selection;
+ }
+
+ public int[][] getVisibleRegionBoundaries(int min, int max)
+ {
+ Vector regions = new Vector();
+ int start = min;
+ int end = max;
+
+ do
+ {
+ if (hasHiddenColumns)
+ {
+ if (start == 0)
+ {
+ start = colSel.adjustForHiddenColumns(start);
+ }
+
+ end = colSel.getHiddenBoundaryRight(start);
+ if (start == end)
+ {
+ end = max;
+ }
+ if (end > max)
+ {
+ end = max;
+ }
+ }
+
+ regions.addElement(new int[]
+ { start, end });
+
+ if (hasHiddenColumns)
+ {
+ start = colSel.adjustForHiddenColumns(end);
+ start = colSel.getHiddenBoundaryLeft(start) + 1;
+ }
+ } while (end < max);
+
+ int[][] startEnd = new int[regions.size()][2];
+
+ regions.copyInto(startEnd);
+
+ return startEnd;
+
+ }
+
+ public boolean getShowHiddenMarkers()
+ {
+ return showHiddenMarkers;
+ }
+
+ public void setShowHiddenMarkers(boolean show)
+ {
+ showHiddenMarkers = show;
+ }
+
+ public String getSequenceSetId()
+ {
+ if (sequenceSetID == null)
+ {
+ sequenceSetID = alignment.hashCode() + "";
+ }
+
+ return sequenceSetID;
+ }
+
+ /**
+ * unique viewId for synchronizing state with stored Jalview Project
+ *
+ */
+ private String viewId = null;
+
+ public String getViewId()
+ {
+ if (viewId == null)
+ {
+ viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
+ }
+ return viewId;
+ }
+
+ public void alignmentChanged(AlignmentPanel ap)
+ {
+ if (padGaps)
+ {
+ alignment.padGaps();
+ }
+ if (hconsensus != null && autoCalculateConsensus)
+ {
+ updateConservation(ap);
+ }
+ if (autoCalculateConsensus)
+ {
+ updateConsensus(ap);
+ }
+ if (autoCalculateStrucConsensus)
+ {
+ updateStrucConsensus(ap);
+ }
+
+ // Reset endRes of groups if beyond alignment width
+ int alWidth = alignment.getWidth();
+ Vector groups = alignment.getGroups();
+ if (groups != null)
+ {
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ if (sg.getEndRes() > alWidth)
+ {
+ sg.setEndRes(alWidth - 1);
+ }
+ }
+ }
+
+ if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
+ {
+ selectionGroup.setEndRes(alWidth - 1);
+ }
+
+ resetAllColourSchemes();
+
+ // alignment.adjustSequenceAnnotations();
+ }
+
+ void resetAllColourSchemes()
+ {
+ ColourSchemeI cs = globalColourScheme;
+ if (cs != null)
+ {
+ if (cs instanceof ClustalxColourScheme)
+ {
+ ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
+ alignment.getWidth());
+ }
+
+ cs.setConsensus(hconsensus);
+ if (cs.conservationApplied())
+ {
+ Alignment al = (Alignment) alignment;
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3, al.getSequences(), 0, al
+ .getWidth() - 1);
+ c.calculate();
+ c.verdict(false, ConsPercGaps);
+
+ cs.setConservation(c);
+ }
+ }
+
+ int s, sSize = alignment.getGroups().size();
+ for (s = 0; s < sSize; s++)
+ {
+ SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
+ if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
+ {
+ ((ClustalxColourScheme) sg.cs).resetClustalX(sg
+ .getSequences(hiddenRepSequences), sg.getWidth());
+ }
+ sg.recalcConservation();
+ }
+ }
+
+ public Color getSequenceColour(SequenceI seq)
+ {
+ if (sequenceColours == null || !sequenceColours.containsKey(seq))
+ {
+ return Color.white;
+ }
+ else
+ {
+ return (Color) sequenceColours.get(seq);
+ }
+ }
+
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+
+ if (col == null)
+ {
+ sequenceColours.remove(seq);
+ }
+ else
+ {
+ sequenceColours.put(seq, col);
+ }
+ }
+
+ /**
+ * returns the visible column regions of the alignment
+ *
+ * @param selectedRegionOnly
+ * true to just return the contigs intersecting with the selected
+ * area
+ * @return
+ */
+ public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ {
+ int[] viscontigs = null;
+ int start = 0, end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ viscontigs = colSel.getVisibleContigs(start, end);
+ return viscontigs;
+ }
+
+ /**
+ * get hash of undo and redo list for the alignment
+ *
+ * @return long[] { historyList.hashCode, redoList.hashCode };
+ */
+ public long[] getUndoRedoHash()
+ {
+ if (historyList == null || redoList == null)
+ return new long[]
+ { -1, -1 };
+ return new long[]
+ { historyList.hashCode(), this.redoList.hashCode() };
+ }
+
+ /**
+ * test if a particular set of hashcodes are different to the hashcodes for
+ * the undo and redo list.
+ *
+ * @param undoredo
+ * the stored set of hashcodes as returned by getUndoRedoHash
+ * @return true if the hashcodes differ (ie the alignment has been edited) or
+ * the stored hashcode array differs in size
+ */
+ public boolean isUndoRedoHashModified(long[] undoredo)
+ {
+ if (undoredo == null)
+ {
+ return true;
+ }
+ long[] cstate = getUndoRedoHash();
+ if (cstate.length != undoredo.length)
+ {
+ return true;
+ }
+
+ for (int i = 0; i < cstate.length; i++)
+ {
+ if (cstate[i] != undoredo[i])
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public boolean getCentreColumnLabels()
+ {
+ return centreColumnLabels;
+ }
+
+ public void setCentreColumnLabels(boolean centrecolumnlabels)
+ {
+ centreColumnLabels = centrecolumnlabels;
+ }
+
+ public void updateSequenceIdColours()
+ {
+ Vector groups = alignment.getGroups();
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+ for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
+ if (sg.idColour != null)
+ {
+ Vector sqs = sg.getSequences(hiddenRepSequences);
+ for (int s = 0, sSize = sqs.size(); s < sSize; s++)
+ {
+ sequenceColours.put(sqs.elementAt(s), sg.idColour);
+ }
+ }
+ }
+ }
+
+ /**
+ * enable or disable the display of Database Cross References in the sequence
+ * ID tooltip
+ */
+ public void setShowDbRefs(boolean show)
+ {
+ showdbrefs = show;
+ }
+
+ /**
+ *
+ * @return true if Database References are to be displayed on tooltips.
+ */
+ public boolean isShowDbRefs()
+ {
+ return showdbrefs;
+ }
+
+ /**
+ *
+ * @return true if Non-positional features are to be displayed on tooltips.
+ */
+ public boolean isShowNpFeats()
+ {
+ return shownpfeats;
+ }
+
+ /**
+ * enable or disable the display of Non-Positional sequence features in the
+ * sequence ID tooltip
+ *
+ * @param show
+ */
+ public void setShowNpFeats(boolean show)
+ {
+ shownpfeats = show;
+ }
+
+ /**
+ *
+ * @return true if view has hidden rows
+ */
+ public boolean hasHiddenRows()
+ {
+ return hasHiddenRows;
+ }
+
+ /**
+ *
+ * @return true if view has hidden columns
+ */
+ public boolean hasHiddenColumns()
+ {
+ return hasHiddenColumns;
+ }
+
+ /**
+ * when set, view will scroll to show the highlighted position
+ */
+ public boolean followHighlight = true;
+
+ /**
+ * @return true if view should scroll to show the highlighted region of a
+ * sequence
+ * @return
+ */
+ public boolean getFollowHighlight()
+ {
+ return followHighlight;
+ }
+
+ public boolean followSelection = true;
+
+ /**
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
+ */
+ public boolean getFollowSelection()
+ {
+ return followSelection;
+ }
+
+ private long sgrouphash = -1, colselhash = -1;
+
+ boolean showSeqFeaturesHeight;
+
+ /**
+ * checks current SelectionGroup against record of last hash value, and
+ * updates record.
+ *
+ * @param b
+ * update the record of last hash value
+ *
+ * @return true if SelectionGroup changed since last call (when b is true)
+ */
+ boolean isSelectionGroupChanged(boolean b)
+ {
+ int hc = (selectionGroup == null || selectionGroup.getSize() == 0) ? -1
+ : selectionGroup.hashCode();
+ if (hc != -1 && hc != sgrouphash)
+ {
+ if (b)
+ {
+ sgrouphash = hc;
+ }
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * checks current colsel against record of last hash value, and optionally
+ * updates record.
+ *
+ * @param b
+ * update the record of last hash value
+ * @return true if colsel changed since last call (when b is true)
+ */
+ boolean isColSelChanged(boolean b)
+ {
+ int hc = (colSel == null || colSel.size() == 0) ? -1 : colSel
+ .hashCode();
+ if (hc != -1 && hc != colselhash)
+ {
+ if (b)
+ {
+ colselhash = hc;
+ }
+ return true;
+ }
+ return false;
+ }
+
+ public void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
+ }
+
+ public void setShowSequenceFeaturesHeight(boolean selected)
+ {
+ showSeqFeaturesHeight = selected;
+ }
+
+ public boolean getShowSequenceFeaturesHeight()
+ {
+ return showSeqFeaturesHeight;
+ }
+
+ boolean showUnconserved = false;
+
+ public boolean getShowUnconserved()
+ {
+ return showUnconserved;
+ }
+
+ public void setShowUnconserved(boolean showunconserved)
+ {
+ showUnconserved = showunconserved;
+ }
+
+ /**
+ * return the alignPanel containing the given viewport. Use this to get the
+ * components currently handling the given viewport.
+ *
+ * @param av
+ * @return null or an alignPanel guaranteed to have non-null alignFrame
+ * reference
+ */
+ public AlignmentPanel getAlignPanel()
+ {
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+ .getSequenceSetId());
+ AlignmentPanel ap = null;
+ for (int p = 0; aps != null && p < aps.length; p++)
+ {
+ if (aps[p].av == this)
+ {
+ return aps[p];
+ }
+ }
+ return null;
+ }
+
+ public boolean getSortByTree()
+ {
+ return sortByTree;
+ }
+
+ public void setSortByTree(boolean sort)
+ {
+ sortByTree = sort;
+ }
+
+ /**
+ * should conservation rows be shown for groups
+ */
+ boolean showGroupConservation = false;
+
+ /**
+ * should consensus rows be shown for groups
+ */
+ boolean showGroupConsensus = false;
+
+ /**
+ * should consensus profile be rendered by default
+ */
+ public boolean showSequenceLogo = false;
+
+ /**
+ * should consensus histograms be rendered by default
+ */
+ public boolean showConsensusHistogram = true;
+
+ /**
+ * @return the showConsensusProfile
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return showSequenceLogo;
+ }
+
+ /**
+ * @param showSequenceLogo
+ * the new value
+ */
+ public void setShowSequenceLogo(boolean showSequenceLogo)
+ {
+ if (showSequenceLogo != this.showSequenceLogo)
+ {
+ // TODO: decouple settings setting from calculation when refactoring
+ // annotation update method from alignframe to viewport
+ this.showSequenceLogo = showSequenceLogo;
+ if (consensusThread != null)
+ {
+ consensusThread.updateAnnotation();
+ }
+ if (strucConsensusThread != null)
+ {
+ strucConsensusThread.updateAnnotation();
+ }
+ }
+ this.showSequenceLogo = showSequenceLogo;
+ }
+
+ /**
+ * @param showConsensusHistogram
+ * the showConsensusHistogram to set
+ */
+ public void setShowConsensusHistogram(boolean showConsensusHistogram)
+ {
+ this.showConsensusHistogram = showConsensusHistogram;
+ }
+
+ /**
+ * @return the showGroupConservation
+ */
+ public boolean isShowGroupConservation()
+ {
+ return showGroupConservation;
+ }
+
+ /**
+ * @param showGroupConservation
+ * the showGroupConservation to set
+ */
+ public void setShowGroupConservation(boolean showGroupConservation)
+ {
+ this.showGroupConservation = showGroupConservation;
+ }
+
+ /**
+ * @return the showGroupConsensus
+ */
+ public boolean isShowGroupConsensus()
+ {
+ return showGroupConsensus;
+ }
+
+ /**
+ * @param showGroupConsensus
+ * the showGroupConsensus to set
+ */
+ public void setShowGroupConsensus(boolean showGroupConsensus)
+ {
+ this.showGroupConsensus = showGroupConsensus;
+ }
+
+ /**
+ *
+ * @return flag to indicate if the consensus histogram should be rendered by
+ * default
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return this.showConsensusHistogram;
+ }
+
+ /**
+ * synthesize a column selection if none exists so it covers the given
+ * selection group. if wholewidth is false, no column selection is made if the
+ * selection group covers the whole alignment width.
+ *
+ * @param sg
+ * @param wholewidth
+ */
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+ {
+ int sgs, sge;
+ if (sg != null
+ && (sgs = sg.getStartRes()) >= 0
+ && sg.getStartRes() <= (sge = sg.getEndRes())
+ && (colSel == null || colSel.getSelected() == null || colSel
+ .getSelected().size() == 0))
+ {
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+ {
+ // do nothing
+ return;
+ }
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
+ }
+ }
+ }
+
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ }
+
+ /**
+ *
+ * @param pdbEntries
+ * @return a series of SequenceI arrays, one for each PDBEntry, listing which
+ * sequence in the alignment holds a reference to it
+ */
+ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+ {
+ ArrayList<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ for (PDBEntry pdb : pdbEntries)
+ {
+ ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+ for (int i = 0; i < alignment.getHeight(); i++)
+ {
+ Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
+ .getPDBId();
+ if (pdbs == null)
+ continue;
+ SequenceI sq;
+ for (int p = 0; p < pdbs.size(); p++)
+ {
+ PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq = alignment.getSequenceAt(i)))
+ seqs.add(sq);
+
+ continue;
+ }
+ }
+ }
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff