-/*\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 java.util.*;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.analysis.*;\r
-import jalview.bin.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-\r
-public class AlignViewport\r
-{\r
- int startRes;\r
- int endRes;\r
- int startSeq;\r
- int endSeq;\r
- boolean showFullId = false;\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 = new SequenceGroup();\r
- int charHeight;\r
- int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
- Font font = new Font("SansSerif", Font.PLAIN, 10);\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
- public Vector vconsensus;\r
- AlignmentAnnotation consensus;\r
- AlignmentAnnotation conservation;\r
- AlignmentAnnotation quality;\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.\r
- PropertyChangeSupport(this);\r
-\r
- public AlignViewport(AlignmentI al)\r
- {\r
- setAlignment(al);\r
- this.startRes = 0;\r
- this.endRes = al.getWidth() - 1;\r
- this.startSeq = 0;\r
- this.endSeq = al.getHeight() - 1;\r
-\r
- updateFromPreferences();\r
- }\r
-\r
- public void updateFromPreferences()\r
- {\r
- showFullId = Preferences.showFullId;\r
- showAnnotation = Preferences.showAnnotation;\r
- showConservation = Preferences.showConservation;\r
- showQuality = Preferences.showQuality;\r
- showIdentity = Preferences.showIdentity;\r
- showFullId = Preferences.showFullId;\r
-\r
- String fontName = Preferences.fontName;\r
- String fontStyle = Preferences.fontStyle;\r
- String fontSize = Cache.getProperty("FONT_SIZE");\r
-\r
- if ( (fontName != null) && (fontStyle != null) && (fontSize != null))\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
- else\r
- {\r
- setFont(font);\r
- }\r
-\r
- alignment.setGapCharacter(Preferences.gapSymbol);\r
-\r
- // We must set conservation and consensus before setting colour,\r
- // as Blosum and Clustal require this to be done\r
- updateConservation();\r
- updateConsensus();\r
-\r
- if (Preferences.defaultColour != null)\r
- {\r
- globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
- Preferences.defaultColour);\r
-\r
- if (globalColourScheme instanceof UserColourScheme)\r
- {\r
- globalColourScheme = UserDefinedColours.loadDefaultColours();\r
- }\r
-\r
- if (globalColourScheme != null)\r
- {\r
- globalColourScheme.setConsensus(vconsensus);\r
- }\r
- }\r
- }\r
-\r
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\r
- }\r
-\r
- public void updateConservation()\r
- {\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
- 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
- 1);\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(), 1);\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
-\r
- public void updateConsensus()\r
- {\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 = Float.parseFloat(hash.get("maxCount").toString());\r
- value /= Float.parseFloat(hash.get("size").toString());\r
-\r
- value *= 100;\r
-\r
- String maxRes = hash.get("maxResidue") + " ";\r
- String mouseOver = hash.get("maxResidue") + " ";\r
-\r
- if (maxRes.length() > 2)\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, 1);\r
-\r
- if (showIdentity)\r
- {\r
- alignment.addAnnotation(consensus);\r
- }\r
- }\r
- else\r
- {\r
- consensus.annotations = annotations;\r
- }\r
- }\r
-\r
- public SequenceGroup getSelectionGroup()\r
- {\r
- return selectionGroup;\r
- }\r
-\r
- public void setSelectionGroup(SequenceGroup sg)\r
- {\r
- selectionGroup = sg;\r
- }\r
-\r
- public boolean getConservationSelected()\r
- {\r
- return conservationColourSelected;\r
- }\r
-\r
- public void setConservationSelected(boolean b)\r
- {\r
- conservationColourSelected = b;\r
- }\r
-\r
- public boolean getAbovePIDThreshold()\r
- {\r
- return abovePIDThreshold;\r
- }\r
-\r
- public void setAbovePIDThreshold(boolean b)\r
- {\r
- abovePIDThreshold = b;\r
- }\r
-\r
- public int getStartRes()\r
- {\r
- return startRes;\r
- }\r
-\r
- public int getEndRes()\r
- {\r
- return endRes;\r
- }\r
-\r
- public int getStartSeq()\r
- {\r
- return startSeq;\r
- }\r
-\r
- public void setGlobalColourScheme(ColourSchemeI cs)\r
- {\r
- globalColourScheme = cs;\r
- }\r
-\r
- public ColourSchemeI getGlobalColourScheme()\r
- {\r
- return globalColourScheme;\r
- }\r
-\r
- public void setStartRes(int res)\r
- {\r
- this.startRes = res;\r
- }\r
-\r
- public void setStartSeq(int seq)\r
- {\r
- this.startSeq = seq;\r
- }\r
-\r
- public void setEndRes(int res)\r
- {\r
- if (res > (alignment.getWidth() - 1))\r
- {\r
- // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth() - 1;\r
- }\r
-\r
- if (res < 0)\r
- {\r
- res = 0;\r
- }\r
-\r
- this.endRes = res;\r
- }\r
-\r
- public void setEndSeq(int seq)\r
- {\r
- if (seq > alignment.getHeight())\r
- {\r
- seq = alignment.getHeight();\r
- }\r
-\r
- if (seq < 0)\r
- {\r
- seq = 0;\r
- }\r
-\r
- this.endSeq = seq;\r
- }\r
-\r
- public int getEndSeq()\r
- {\r
- return endSeq;\r
- }\r
-\r
- public void setFont(Font f)\r
- {\r
- font = f;\r
-\r
- javax.swing.JFrame temp = new javax.swing.JFrame();\r
- temp.addNotify();\r
-\r
- java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);\r
- setCharHeight(fm.getHeight());\r
- setCharWidth(fm.charWidth('M'));\r
- }\r
-\r
- public Font getFont()\r
- {\r
- return font;\r
- }\r
-\r
- public void setCharWidth(int w)\r
- {\r
- this.charWidth = w;\r
- }\r
-\r
- public int getCharWidth()\r
- {\r
- return charWidth;\r
- }\r
-\r
- public void setCharHeight(int h)\r
- {\r
- this.charHeight = h;\r
- }\r
-\r
- public int getCharHeight()\r
- {\r
- return charHeight;\r
- }\r
-\r
- public void setChunkWidth(int w)\r
- {\r
- this.chunkWidth = w;\r
- }\r
-\r
- public int getChunkWidth()\r
- {\r
- return chunkWidth;\r
- }\r
-\r
- public void setChunkHeight(int h)\r
- {\r
- this.chunkHeight = h;\r
- }\r
-\r
- public int getChunkHeight()\r
- {\r
- return chunkHeight;\r
- }\r
-\r
- public AlignmentI getAlignment()\r
- {\r
- return alignment;\r
- }\r
-\r
- public void setAlignment(AlignmentI align)\r
- {\r
- this.alignment = align;\r
- }\r
-\r
- public void setWrapAlignment(boolean state)\r
- {\r
- wrapAlignment = state;\r
- }\r
-\r
- public void setShowText(boolean state)\r
- {\r
- showText = state;\r
- }\r
-\r
- public void setRenderGaps(boolean state)\r
- {\r
- renderGaps = state;\r
- }\r
-\r
- public boolean getColourText()\r
- {\r
- return showColourText;\r
- }\r
-\r
- public void setColourText(boolean state)\r
- {\r
- showColourText = state;\r
- }\r
-\r
- public void setShowBoxes(boolean state)\r
- {\r
- showBoxes = state;\r
- }\r
-\r
- public boolean getWrapAlignment()\r
- {\r
- return wrapAlignment;\r
- }\r
-\r
- public boolean getShowText()\r
- {\r
- return showText;\r
- }\r
-\r
- public boolean getShowBoxes()\r
- {\r
- return showBoxes;\r
- }\r
-\r
- public char getGapCharacter()\r
- {\r
- return getAlignment().getGapCharacter();\r
- }\r
-\r
- public void setGapCharacter(char gap)\r
- {\r
- if (getAlignment() != null)\r
- {\r
- getAlignment().setGapCharacter(gap);\r
- }\r
- }\r
-\r
- public void setThreshold(int thresh)\r
- {\r
- threshold = thresh;\r
- }\r
-\r
- public int getThreshold()\r
- {\r
- return threshold;\r
- }\r
-\r
- public void setIncrement(int inc)\r
- {\r
- increment = inc;\r
- }\r
-\r
- public int getIncrement()\r
- {\r
- return increment;\r
- }\r
-\r
- public 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
- public ColumnSelection getColumnSelection()\r
- {\r
- return colSel;\r
- }\r
-\r
- public void resetSeqLimits(int height)\r
- {\r
- setEndSeq(height / getCharHeight());\r
- }\r
-\r
- public void setCurrentTree(NJTree tree)\r
- {\r
- currentTree = tree;\r
- }\r
-\r
- public NJTree getCurrentTree()\r
- {\r
- return currentTree;\r
- }\r
-\r
- public void setColourAppliesToAllGroups(boolean b)\r
- {\r
- colourAppliesToAllGroups = b;\r
- }\r
-\r
- public boolean getColourAppliesToAllGroups()\r
- {\r
- return colourAppliesToAllGroups;\r
- }\r
-\r
- public boolean getShowFullId()\r
- {\r
- return showFullId;\r
- }\r
-\r
- public void setShowFullId(boolean b)\r
- {\r
- showFullId = b;\r
- }\r
-\r
- public boolean getShowAnnotation()\r
- {\r
- return showAnnotation;\r
- }\r
-\r
- public void setShowAnnotation(boolean b)\r
- {\r
- showAnnotation = b;\r
- }\r
-\r
- public boolean getScaleAboveWrapped()\r
- {\r
- return scaleAboveWrapped;\r
- }\r
-\r
- public boolean getScaleLeftWrapped()\r
- {\r
- return scaleLeftWrapped;\r
- }\r
-\r
- public boolean getScaleRightWrapped()\r
- {\r
- return scaleRightWrapped;\r
- }\r
-\r
- public void setScaleAboveWrapped(boolean b)\r
- {\r
- scaleAboveWrapped = b;\r
- }\r
-\r
- public void setScaleLeftWrapped(boolean b)\r
- {\r
- scaleLeftWrapped = b;\r
- }\r
-\r
- public void setScaleRightWrapped(boolean b)\r
- {\r
- scaleRightWrapped = b;\r
- }\r
-\r
- public void addPropertyChangeListener(\r
- java.beans.PropertyChangeListener listener)\r
- {\r
- changeSupport.addPropertyChangeListener(listener);\r
- }\r
-\r
- public void removePropertyChangeListener(\r
- java.beans.PropertyChangeListener listener)\r
- {\r
- changeSupport.removePropertyChangeListener(listener);\r
- }\r
-\r
- public void firePropertyChange(String prop, Object oldvalue, Object newvalue)\r
- {\r
- changeSupport.firePropertyChange(prop, oldvalue, newvalue);\r
- }\r
-}\r
+ /*
+ * 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.bin.*;
+
+import jalview.datamodel.*;
+
+import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AlignViewport
+{
+ 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;
+
+ // The following vector holds the features which are
+ // currently visible, in the correct order or rendering
+ Hashtable featuresDisplayed = null;
+
+
+ /** DOCUMENT ME!! */
+ public Hashtable [] hconsensus;
+ AlignmentAnnotation consensus;
+ AlignmentAnnotation conservation;
+ AlignmentAnnotation quality;
+ boolean autoCalculateConsensus = 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;
+
+
+ /**
+ * Creates a new AlignViewport object.
+ *
+ * @param al DOCUMENT ME!
+ */
+ public AlignViewport(AlignmentI al)
+ {
+ 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)
+ {
+ hasHiddenColumns = true;
+ }
+ }
+ 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);
+
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
+
+ padGaps = Cache.getDefault("PAD_GAPS", 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);
+ }
+ }
+
+ consensus = new AlignmentAnnotation("Consensus", "PID",
+ new Annotation[1], 0f, 100f,
+ AlignmentAnnotation.BAR_GRAPH);
+ consensus.hasText = true;
+ consensus.autoCalculated=true;
+
+ if (Cache.getDefault("SHOW_IDENTITY", true))
+ {
+ alignment.addAnnotation(consensus);
+ }
+ }
+
+ 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);
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setShowSequenceFeatures(boolean b)
+ {
+ showSequenceFeatures = b;
+ }
+
+ public boolean getShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+ class ConservationThread
+ extends Thread
+ {
+ AlignmentPanel ap;
+ public ConservationThread(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ }
+
+ public void run()
+ {
+ try
+ {
+ updatingConservation = true;
+
+ while (UPDATING_CONSERVATION)
+ {
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false);
+ }
+ Thread.sleep(200);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ UPDATING_CONSERVATION = true;
+
+
+ int alWidth = alignment.getWidth();
+ if(alWidth<0)
+ {
+ return;
+ }
+
+ Conservation cons = new jalview.analysis.Conservation("All",
+ jalview.schemes.ResidueProperties.propHash, 3,
+ alignment.getSequences(), 0, alWidth -1);
+
+ cons.calculate();
+ cons.verdict(false, ConsPercGaps);
+
+ if (quality!=null)
+ {
+ cons.findQuality();
+ }
+
+ char [] sequence = cons.getConsSequence().getSequence();
+ float minR;
+ float minG;
+ float minB;
+ float maxR;
+ float maxG;
+ float maxB;
+ minR = 0.3f;
+ minG = 0.0f;
+ minB = 0f;
+ maxR = 1.0f - minR;
+ maxG = 0.9f - minG;
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality
+
+ float min = 0f;
+ float max = 11f;
+ float qmin = 0f;
+ float qmax = 0f;
+
+ char c;
+
+ conservation.annotations = new Annotation[alWidth];
+
+ if (quality!=null)
+ {
+ quality.graphMax = cons.qualityRange[1].floatValue();
+ quality.annotations = new Annotation[alWidth];
+ qmin = cons.qualityRange[0].floatValue();
+ qmax = cons.qualityRange[1].floatValue();
+ }
+
+ for (int i = 0; i < alWidth; i++)
+ {
+ float value = 0;
+
+ c = sequence[i];
+
+ if (Character.isDigit(c))
+ {
+ value = (int) (c - '0');
+ }
+ else if (c == '*')
+ {
+ value = 11;
+ }
+ else if (c == '+')
+ {
+ value = 10;
+ }
+
+ float vprop = value - min;
+ vprop /= max;
+ conservation.annotations[i] =
+ new Annotation(String.valueOf(c),
+ String.valueOf(value), ' ', value,
+ new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop),
+ minB + (maxB * vprop)));
+
+ // Quality calc
+ if (quality!=null)
+ {
+ value = ( (Double) cons.quality.get(i)).floatValue();
+ vprop = value - qmin;
+ vprop /= qmax;
+ quality.annotations[i] = new Annotation(" ", String.valueOf(value),
+ ' ',
+ value,
+ new Color(minR + (maxR * vprop),
+ minG + (maxG * vprop),
+ minB + (maxB * vprop)));
+ }
+ }
+ }
+ catch (OutOfMemoryError error)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+
+
+ public void run()
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory calculating conservation!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
+
+ conservation = null;
+ quality = null;
+
+ System.out.println("Conservation calculation: " + error);
+ System.gc();
+
+ }
+
+ UPDATING_CONSERVATION = false;
+ updatingConservation = false;
+
+ if(ap!=null)
+ {
+ ap.paintAlignment(true);
+ }
+
+ }
+ }
+
+
+ ConservationThread conservationThread;
+
+ ConsensusThread consensusThread;
+
+ boolean consUpdateNeeded = false;
+
+ static boolean UPDATING_CONSENSUS = false;
+
+ static boolean UPDATING_CONSERVATION = false;
+
+ boolean updatingConsensus = false;
+
+ boolean updatingConservation = false;
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateConservation(final AlignmentPanel ap)
+ {
+ if (alignment.isNucleotide() || conservation==null)
+ {
+ return;
+ }
+
+ conservationThread = new ConservationThread(ap);
+ conservationThread.start();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void updateConsensus(final AlignmentPanel ap)
+ {
+ 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.getWidth();
+ if(aWidth<0)
+ {
+ return;
+ }
+
+ consensus.annotations = null;
+ consensus.annotations = new Annotation[aWidth];
+
+
+ hconsensus = new Hashtable[aWidth];
+ AAFrequency.calculate(alignment.getSequencesArray(),
+ 0,
+ alignment.getWidth(),
+ hconsensus);
+
+ for (int i = 0; i < aWidth; i++)
+ {
+ float value = 0;
+ if (ignoreGapsInConsensusCalculation)
+ {
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)).
+ floatValue();
+ }
+ else
+ {
+ value = ( (Float) hconsensus[i].get(AAFrequency.PID_GAPS)).
+ floatValue();
+ }
+
+ String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString();
+ String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " ";
+
+ if (maxRes.length() > 1)
+ {
+ mouseOver = "[" + maxRes + "] ";
+ maxRes = "+";
+ }
+
+ mouseOver += ( (int) value + "%");
+ consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ',
+ value);
+ }
+
+
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
+
+ }
+ catch (OutOfMemoryError error)
+ {
+ alignment.deleteAnnotation(consensus);
+
+ consensus = null;
+ hconsensus = null;
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Out of memory calculating consensus!!"
+ +
+ "\nSee help files for increasing Java Virtual Machine memory."
+ , "Out of memory",
+ javax.swing.JOptionPane.WARNING_MESSAGE);
+ }
+ });
+
+ System.out.println("Consensus calculation: " + error);
+ System.gc();
+ }
+ UPDATING_CONSENSUS = false;
+ updatingConsensus = false;
+
+ if (ap != null)
+ {
+ ap.paintAlignment(true);
+ }
+ }
+ }
+ /**
+ * 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;
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceGroup getSelectionGroup()
+ {
+ return selectionGroup;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sg DOCUMENT ME!
+ */
+ public void setSelectionGroup(SequenceGroup sg)
+ {
+ selectionGroup = sg;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getConservationSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setConservationSelected(boolean b)
+ {
+ conservationColourSelected = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getAbovePIDThreshold()
+ {
+ return abovePIDThreshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ 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().removeMappings(alignment.getCodonFrames());
+ }
+ this.alignment = align;
+ if (alignment.getCodonFrames()!=null)
+ {
+ StructureSelectionManager.getStructureSelectionManager().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);
+ }
+ }
+
+ 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());
+ }
+
+ 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());
+ 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;
+ if (selectionGroup==null)
+ {
+ sequences = alignment.getSequencesArray();
+ }
+ else
+ {
+ sequences = selectionGroup.getSequencesInOrder(alignment);
+ }
+ return sequences;
+ }
+ /**
+ * This method returns the visible alignment as text, as
+ * seen on the GUI, ie if columns are hidden they will not
+ * be returned in the result.
+ * Use this for calculating trees, PCA, redundancy etc on views
+ * which contain hidden columns.
+ * @return String[]
+ */
+ public jalview.datamodel.CigarArray getViewAsCigars(boolean
+ selectedRegionOnly)
+ {
+ CigarArray selection=null;
+ SequenceI [] seqs= null;
+ int i, iSize;
+ int start = 0, end = 0;
+ if(selectedRegionOnly && selectionGroup!=null)
+ {
+ iSize = selectionGroup.getSize();
+ seqs = selectionGroup.getSequencesInOrder(alignment);
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes(); // inclusive for start and end in SeqCigar constructor
+ }
+ else
+ {
+ iSize = alignment.getHeight();
+ seqs = alignment.getSequencesArray();
+ end = alignment.getWidth()-1;
+ }
+ SeqCigar[] selseqs = new SeqCigar[iSize];
+ for(i=0; i<iSize; i++)
+ {
+ selseqs[i] = new SeqCigar(seqs[i], start, end);
+ }
+ selection=new CigarArray(selseqs);
+ // now construct the CigarArray operations
+ if (hasHiddenColumns)
+ {
+ Vector regions = colSel.getHiddenColumns();
+ int [] region;
+ int hideStart, hideEnd;
+ int last=start;
+ for (int j = 0; last<end & j < regions.size(); j++)
+ {
+ region = (int[]) regions.elementAt(j);
+ hideStart = region[0];
+ hideEnd = region[1];
+ // edit hidden regions to selection range
+ if (hideStart < last)
+ {
+ if (hideEnd > last)
+ {
+ hideStart = last;
+ }
+ else
+ {
+ continue;
+ }
+ }
+
+ if (hideStart>end)
+ {
+ break;
+ }
+
+ if (hideEnd>end)
+ {
+ hideEnd=end;
+ }
+
+ if (hideStart>hideEnd)
+ {
+ break;
+ }
+ /**
+ * form operations...
+ */
+ if (last<hideStart)
+ {
+ selection.addOperation(CigarArray.M, hideStart-last);
+ }
+ selection.addOperation(CigarArray.D, 1+hideEnd-hideStart);
+ last = hideEnd+1;
+ }
+ // Final match if necessary.
+ if (last<end)
+ {
+ selection.addOperation(CigarArray.M, end-last+1);
+ }
+ }
+ else
+ {
+ selection.addOperation(CigarArray.M, end-start+1);
+ }
+ return selection;
+ }
+ /**
+ * return a compact representation of the current alignment selection to
+ * pass to an analysis function
+ * @param selectedOnly boolean true to just return the selected view
+ * @return AlignmentView
+ */
+ jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+ {
+ // JBPNote:
+ // this is here because the AlignmentView constructor modifies the CigarArray
+ // object. Refactoring of Cigar and alignment view representation should
+ // be done to remove redundancy.
+ CigarArray aligview = getViewAsCigars(selectedOnly);
+ if (aligview != null)
+ {
+ return new AlignmentView(aligview,
+ (selectedOnly && selectionGroup != null) ?
+ selectionGroup.getStartRes() : 0);
+ }
+ return null;
+ }
+ /**
+ * This method returns the visible alignment as text, as
+ * seen on the GUI, ie if columns are hidden they will not
+ * be returned in the result.
+ * Use this for calculating trees, PCA, redundancy etc on views
+ * which contain hidden columns.
+ * @return String[]
+ */
+ public String [] getViewAsString(boolean selectedRegionOnly)
+ {
+ String [] selection = null;
+ SequenceI [] seqs= null;
+ int i, iSize;
+ int start = 0, end = 0;
+ if(selectedRegionOnly && selectionGroup!=null)
+ {
+ iSize = selectionGroup.getSize();
+ 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;
+ }
+
+ public void alignmentChanged(AlignmentPanel ap)
+ {
+ if (padGaps)
+ {
+ alignment.padGaps();
+ }
+
+ if (hconsensus != null && autoCalculateConsensus)
+ {
+ updateConsensus(ap);
+ updateConservation(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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff