- /*\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
- 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
- * DOCUMENT ME!\r
- *\r
- * @param y DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getIndex(int y)\r
- {\r
- int y1 = 0;\r
- int starty = getStartSeq();\r
- int endy = getEndSeq();\r
-\r
- for (int i = starty; i <= endy; i++)\r
- {\r
- if ((i < alignment.getHeight()) &&\r
- (alignment.getSequenceAt(i) != null))\r
- {\r
- int y2 = y1 + getCharHeight();\r
-\r
- if ((y >= y1) && (y <= y2))\r
- {\r
- return i;\r
- }\r
-\r
- y1 = y2;\r
- }\r
- else\r
- {\r
- return -1;\r
- }\r
- }\r
-\r
- return -1;\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
- while (colSel.size() > 0)\r
- {\r
- int column = ( (Integer) colSel.getSelected().firstElement()).intValue();\r
- colSel.hideColumns(column);\r
- }\r
- setSelectionGroup(null);\r
- hasHiddenColumns = true;\r
- }\r
-\r
-\r
- public void hideColumns(int start, int end)\r
- {\r
- if(start==end)\r
- end++;\r
-\r
- for(int i=start; i<end; i++)\r
- {\r
- colSel.addElement(i);\r
- colSel.hideColumns(i);\r
- }\r
-\r
- setSelectionGroup(null);\r
- hasHiddenColumns = true;\r
- }\r
-\r
- public void hideSequence(SequenceI seq)\r
- {\r
- if(seq!=null)\r
- {\r
- alignment.getHiddenSequences().hideSequence(seq);\r
- hasHiddenRows = true;\r
- }\r
- }\r
-\r
- public void showSequence(int index)\r
- {\r
- alignment.getHiddenSequences().showSequence(index);\r
-\r
- if(alignment.getHiddenSequences().getSize()<1)\r
- hasHiddenRows = false;\r
- }\r
-\r
- public void showColumn(int col)\r
- {\r
- colSel.revealHiddenColumns(col);\r
- if(colSel.size()<1)\r
- hasHiddenColumns = false;\r
- }\r
-\r
- public void showAllHiddenColumns()\r
- {\r
- colSel.revealAllHiddenColumns();\r
- hasHiddenColumns = false;\r
- }\r
-\r
- public void showAllHiddenSeqs()\r
- {\r
- if(alignment.getHiddenSequences().getSize()>0)\r
- {\r
- alignment.getHiddenSequences().showAll();\r
- hasHiddenRows = false;\r
- }\r
- }\r
-\r
- public int adjustForHiddenSeqs(int alignmentIndex)\r
- {\r
- return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);\r
- }\r
-\r
- /**\r
- * This method returns the a new SequenceI [] with\r
- * the selection sequence and start and end points adjusted\r
- * @return String[]\r
- */\r
- public SequenceI[] getSelectionAsNewSequence()\r
- {\r
- SequenceI[] sequences;\r
-\r
- if (selectionGroup == null)\r
- sequences = alignment.getSequencesArray();\r
- else\r
- sequences = selectionGroup.getSelectionAsNewSequences(alignment);\r
-\r
- return sequences;\r
- }\r
-\r
-\r
- /**\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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+/*
+ * 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 jalview.analysis.AlignmentUtils;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
+import jalview.structure.CommandListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.141 $
+ */
+public class AlignViewport extends AlignmentViewport implements
+ SelectionSource, CommandListener
+{
+ Font font;
+
+ NJTree currentTree = null;
+
+ boolean cursorMode = false;
+
+ boolean antiAlias = false;
+
+ private Rectangle explodedGeometry;
+
+ String viewName;
+
+ /*
+ * Flag set true on the view that should 'gather' multiple views of the same
+ * sequence set id when a project is reloaded. Set false on all views when
+ * they are 'exploded' into separate windows. Set true on the current view
+ * when 'Gather' is performed, and also on the first tab when the first new
+ * view is created.
+ */
+ private boolean gatherViewsHere = false;
+
+ private AnnotationColumnChooser annotationColumnSelectionState;
+
+ /**
+ * 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)
+ {
+ colSel = hiddenColumns;
+ }
+ 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)
+ {
+ colSel = hiddenColumns;
+ }
+ init();
+ }
+
+ /**
+ * Apply any settings saved in user preferences
+ */
+ private void applyViewProperties()
+ {
+ antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+
+ viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
+ setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+ setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+ setCentreColumnLabels(Cache.getDefault("CENTRE_COLUMN_LABELS", false));
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+ setPadGaps(Cache.getDefault("PAD_GAPS", true));
+ setShowNPFeats(Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true));
+ setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
+ viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
+ viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
+ viewStyle.setShowUnconserved(Cache
+ .getDefault("SHOW_UNCONSERVED", false));
+ sortByTree = Cache.getDefault("SORT_BY_TREE", false);
+ followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
+ sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
+ Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache.getDefault(
+ Preferences.SHOW_AUTOCALC_ABOVE, false);
+ viewStyle.setScaleProteinAsCdna(Cache.getDefault(
+ Preferences.SCALE_PROTEIN_TO_CDNA, true));
+ }
+
+ void init()
+ {
+ this.startRes = 0;
+ this.endRes = alignment.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = alignment.getHeight() - 1;
+ applyViewProperties();
+
+ String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
+ String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
+ String fontSize = Cache.getDefault("FONT_SIZE", "10");
+
+ int style = 0;
+
+ if (fontStyle.equals("bold"))
+ {
+ style = 1;
+ }
+ else if (fontStyle.equals("italic"))
+ {
+ style = 2;
+ }
+
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
+
+ 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())
+ {
+ showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
+ showQuality = Cache.getDefault("SHOW_QUALITY", true);
+ showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
+ false);
+ }
+ showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
+ true);
+ showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
+ normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+ false);
+ showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
+ showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+ }
+ initAutoAnnotation();
+ String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT;
+ String propertyValue = Cache.getProperty(colourProperty);
+ if (propertyValue == null)
+ {
+ // fall back on this property for backwards compatibility
+ propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+ }
+ if (propertyValue != null)
+ {
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,
+ propertyValue);
+
+ if (globalColourScheme instanceof UserColourScheme)
+ {
+ globalColourScheme = UserDefinedColours.loadDefaultColours();
+ ((UserColourScheme) globalColourScheme).setThreshold(0,
+ isIgnoreGapsConsensus());
+ }
+
+ 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
+ */
+ 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;
+ }
+
+ boolean validCharWidth;
+
+ /**
+ * update view settings with the given font. You may need to call
+ * alignPanel.fontChanged to update the layout geometry
+ *
+ * @param setGrid
+ * when true, charWidth/height is set according to font mentrics
+ */
+ public void setFont(Font f, boolean setGrid)
+ {
+ font = f;
+
+ Container c = new Container();
+
+ java.awt.FontMetrics fm = c.getFontMetrics(font);
+ int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
+ .getCharHeight();
+ if (setGrid)
+ {
+ setCharHeight(fm.getHeight());
+ setCharWidth(ww);
+ }
+ viewStyle.setFontName(font.getName());
+ viewStyle.setFontStyle(font.getStyle());
+ viewStyle.setFontSize(font.getSize());
+
+ validCharWidth = true;
+ }
+
+ @Override
+ public void setViewStyle(ViewStyleI settingsForView)
+ {
+ super.setViewStyle(settingsForView);
+ setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
+ viewStyle.getFontSize()), false);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont()
+ {
+ return font;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align
+ * DOCUMENT ME!
+ */
+ public void setAlignment(AlignmentI align)
+ {
+ replaceMappings(align);
+ this.alignment = align;
+ }
+
+ /**
+ * Replace any codon mappings for this viewport with those for the given
+ * viewport
+ *
+ * @param align
+ */
+ public void replaceMappings(AlignmentI align)
+ {
+
+ /*
+ * Deregister current mappings (if any)
+ */
+ deregisterMappings();
+
+ /*
+ * Register new mappings (if any)
+ */
+ if (align != null)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerMappings(align.getCodonFrames());
+ }
+
+ /*
+ * replace mappings on our alignment
+ */
+ if (alignment != null && align != null)
+ {
+ alignment.setCodonFrames(align.getCodonFrames());
+ }
+ }
+
+ protected void deregisterMappings()
+ {
+ AlignmentI al = getAlignment();
+ if (al != null)
+ {
+ Set<AlignedCodonFrame> mappings = al.getCodonFrames();
+ if (mappings != null)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ for (AlignedCodonFrame acf : mappings)
+ {
+ if (noReferencesTo(acf))
+ {
+ ssm.deregisterMapping(acf);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * 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!
+ *
+ * @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;
+ }
+
+ /**
+ * 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()
+ {
+ // TODO: JAL-1126
+ 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 followSelection = true;
+
+ /**
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
+ */
+ public boolean getFollowSelection()
+ {
+ return followSelection;
+ }
+
+ /**
+ * Send the current selection to be broadcast to any selection listeners.
+ */
+ public void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
+ }
+
+ /**
+ * 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());
+ 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;
+ }
+
+ /**
+ * 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);
+ }
+ }
+ }
+
+ /**
+ * Returns the (Desktop) instance of the StructureSelectionManager
+ */
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ }
+
+ /**
+ *
+ * @param pdbEntries
+ * @return an array of SequenceI arrays, one for each PDBEntry, listing which
+ * sequences in the alignment hold a reference to it
+ */
+ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
+ {
+ List<SequenceI[]> seqvectors = new ArrayList<SequenceI[]>();
+ for (PDBEntry pdb : pdbEntries)
+ {
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+ for (SequenceI sq : alignment.getSequences())
+ {
+ Vector<PDBEntry> pdbs = sq.getDatasetSequence().getAllPDBEntries();
+ if (pdbs == null)
+ {
+ continue;
+ }
+ for (PDBEntry p1 : pdbs)
+ {
+ if (p1.getId().equals(pdb.getId()))
+ {
+ if (!seqs.contains(sq))
+ {
+ seqs.add(sq);
+ continue;
+ }
+ }
+ }
+ }
+ seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+ return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
+ }
+
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
+ /**
+ *
+ * @return true if alignment characters should be displayed
+ */
+ public boolean isValidCharWidth()
+ {
+ return validCharWidth;
+ }
+
+ private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+
+ public AutoCalcSetting getCalcIdSettingsFor(String calcId)
+ {
+ return calcIdParams.get(calcId);
+ }
+
+ public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+ boolean needsUpdate)
+ {
+ calcIdParams.put(calcId, settings);
+ // TODO: create a restart list to trigger any calculations that need to be
+ // restarted after load
+ // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
+ if (needsUpdate)
+ {
+ Cache.log.debug("trigger update for " + calcId);
+ }
+ }
+
+ /**
+ * Method called when another alignment's edit (or possibly other) command is
+ * broadcast to here.
+ *
+ * To allow for sequence mappings (e.g. protein to cDNA), we have to first
+ * 'unwind' the command on the source sequences (in simulation, not in fact),
+ * and then for each edit in turn:
+ * <ul>
+ * <li>compute the equivalent edit on the mapped sequences</li>
+ * <li>apply the mapped edit</li>
+ * <li>'apply' the source edit to the working copy of the source sequences</li>
+ * </ul>
+ *
+ * @param command
+ * @param undo
+ * @param ssm
+ */
+ @Override
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source)
+ {
+ /*
+ * Do nothing unless we are a 'complement' of the source. May replace this
+ * with direct calls not via SSM.
+ */
+ if (source instanceof AlignViewportI
+ && ((AlignViewportI) source).getCodingComplement() == this)
+ {
+ // ok to continue;
+ }
+ else
+ {
+ return;
+ }
+
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+ getGapCharacter());
+ if (mappedCommand != null)
+ {
+ AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
+ mappedCommand.doCommand(views);
+ getAlignPanel().alignmentChanged();
+ }
+ }
+
+ /**
+ * Add the sequences from the given alignment to this viewport. Optionally,
+ * may give the user the option to open a new frame, or split panel, with cDNA
+ * and protein linked.
+ *
+ * @param al
+ * @param title
+ */
+ public void addAlignment(AlignmentI al, String title)
+ {
+ // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
+
+ // JBPComment: title is a largely redundant parameter at the moment
+ // JBPComment: this really should be an 'insert/pre/append' controller
+ // JBPComment: but the DNA/Protein check makes it a bit more complex
+
+ // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
+ // this comment:
+ // TODO: create undo object for this JAL-1101
+
+ /*
+ * If any cDNA/protein mappings can be made between the alignments, offer to
+ * open a linked alignment with split frame option.
+ */
+ if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
+ {
+ if (al.getDataset() == null)
+ {
+ // need to create ds seqs
+ for (SequenceI sq : al.getSequences())
+ {
+ if (sq.getDatasetSequence() == null)
+ {
+ sq.createDatasetSequence();
+ }
+ }
+ }
+ if (AlignmentUtils.isMappable(al, getAlignment()))
+ {
+ if (openLinkedAlignment(al, title))
+ {
+ return;
+ }
+ }
+ }
+
+ /*
+ * No mappings, or offer declined - add sequences to this alignment
+ */
+ // TODO: JAL-407 regardless of above - identical sequences (based on ID and
+ // provenance) should share the same dataset sequence
+
+ for (int i = 0; i < al.getHeight(); i++)
+ {
+ getAlignment().addSequence(al.getSequenceAt(i));
+ }
+
+ setEndSeq(getAlignment().getHeight());
+ firePropertyChange("alignment", null, getAlignment().getSequences());
+ }
+
+ /**
+ * Show a dialog with the option to open and link (cDNA <-> protein) as a new
+ * alignment, either as a standalone alignment or in a split frame. Returns
+ * true if the new alignment was opened, false if not, because the user
+ * declined the offer.
+ *
+ * @param al
+ * @param title
+ */
+ protected boolean openLinkedAlignment(AlignmentI al, String title)
+ {
+ String[] options = new String[] {
+ MessageManager.getString("action.no"),
+ MessageManager.getString("label.split_window"),
+ MessageManager.getString("label.new_window"), };
+ final String question = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.open_split_window?"));
+ int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ MessageManager.getString("label.open_split_window"),
+ JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+
+ if (response != 1 && response != 2)
+ {
+ return false;
+ }
+ final boolean openSplitPane = (response == 1);
+ final boolean openInNewWindow = (response == 2);
+
+ /*
+ * Identify protein and dna alignments. Make a copy of this one if opening
+ * in a new split pane.
+ */
+ AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ : getAlignment();
+ AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+ /*
+ * Map sequences. At least one should get mapped as we have already passed
+ * the test for 'mappability'. Any mappings made will be added to the
+ * protein alignment. Note creating dataset sequences on the new alignment
+ * is a pre-requisite for building mappings.
+ */
+ al.setDataset(null);
+ AlignmentUtils.mapProteinToCdna(protein, cdna);
+
+ /*
+ * Create the AlignFrame for the added alignment. If it is protein, mappings
+ * are registered with StructureSelectionManager as a side-effect.
+ */
+ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ newAlignFrame.setTitle(title);
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new Object[] { title }));
+
+ // TODO if we want this (e.g. to enable reload of the alignment from file),
+ // we will need to add parameters to the stack.
+ // if (!protocol.equals(AppletFormatAdapter.PASTE))
+ // {
+ // alignFrame.setFileName(file, format);
+ // }
+
+ if (openInNewWindow)
+ {
+ Desktop.addInternalFrame(newAlignFrame, title,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ try
+ {
+ newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+
+ if (openSplitPane)
+ {
+ al.alignAs(thisAlignment);
+ protein = openSplitFrame(newAlignFrame, thisAlignment);
+ }
+
+ return true;
+ }
+
+ /**
+ * Helper method to open a new SplitFrame holding linked dna and protein
+ * alignments.
+ *
+ * @param newAlignFrame
+ * containing a new alignment to be shown
+ * @param complement
+ * cdna/protein complement alignment to show in the other split half
+ * @return the protein alignment in the split frame
+ */
+ protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
+ AlignmentI complement)
+ {
+ /*
+ * Make a new frame with a copy of the alignment we are adding to. If this
+ * is protein, the mappings to cDNA will be registered with
+ * StructureSelectionManager as a side-effect.
+ */
+ AlignFrame copyMe = new AlignFrame(complement,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+
+ AlignmentI al = newAlignFrame.viewport.getAlignment();
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+
+ return proteinFrame.viewport.getAlignment();
+ }
+
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
+ {
+ return annotationColumnSelectionState;
+ }
+
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser currentAnnotationColumnSelectionState)
+ {
+ this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
+ }
+
+ @Override
+ public void setIdWidth(int i)
+ {
+ super.setIdWidth(i);
+ AlignmentPanel ap = getAlignPanel();
+ if (ap != null)
+ {
+ // modify GUI elements to reflect geometry change
+ Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
+ .getPreferredSize();
+ idw.width = i;
+ getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+ }
+ }
+
+ public Rectangle getExplodedGeometry()
+ {
+ return explodedGeometry;
+ }
+
+ public void setExplodedGeometry(Rectangle explodedPosition)
+ {
+ this.explodedGeometry = explodedPosition;
+ }
+
+ public boolean isGatherViewsHere()
+ {
+ return gatherViewsHere;
+ }
+
+ public void setGatherViewsHere(boolean gatherViewsHere)
+ {
+ this.gatherViewsHere = gatherViewsHere;
+ }
+
+ /**
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
+ */
+ public void scrollComplementaryAlignment()
+ {
+ /*
+ * Populate a SearchResults object with the mapped location to scroll to. If
+ * there is no complement, or it is not following highlights, or no mapping
+ * is found, the result will be empty.
+ */
+ SearchResults sr = new SearchResults();
+ int verticalOffset = findComplementScrollTarget(sr);
+ if (!sr.isEmpty())
+ {
+ // TODO would like next line without cast but needs more refactoring...
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+ .getAlignPanel();
+ complementPanel.setFollowingComplementScroll(true);
+ complementPanel.scrollToCentre(sr, verticalOffset);
+ }
+ }
+
+ /**
+ * Answers true if no alignment holds a reference to the given mapping
+ *
+ * @param acf
+ * @return
+ */
+ protected boolean noReferencesTo(AlignedCodonFrame acf)
+ {
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames == null)
+ {
+ return true;
+ }
+ for (AlignFrame af : frames)
+ {
+ if (!af.isClosed())
+ {
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ AlignmentI al = ap.getAlignment();
+ if (al != null && al.getCodonFrames().contains(acf))
+ {
+ return false;
+ }
+ }
+ }
+ }
+ return true;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff