+ /*\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.awt.*;\r
import jalview.analysis.*;\r
-import jalview.analysis.NJTree;\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
-\r
- int startSeq;\r
- int endSeq;\r
-\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
-\r
- boolean colourAppliesToAllGroups = true;\r
- ColourSchemeI globalColourScheme = null;\r
- boolean conservationColourSelected = false;\r
- boolean abovePIDThreshold = false;\r
-\r
- SequenceGroup selectionGroup = new SequenceGroup();\r
-\r
- RendererI renderer = new SequenceRenderer(this);\r
-\r
- int charHeight;\r
- int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
-\r
- Font font = new Font("SansSerif",Font.PLAIN,10);\r
- AlignmentI alignment;\r
-\r
- ColumnSelection colSel = new ColumnSelection();\r
-\r
- int threshold;\r
- int increment;\r
-\r
- NJTree currentTree = null;\r
-\r
- boolean scaleAboveWrapped = false;\r
- boolean scaleLeftWrapped = true;\r
- boolean scaleRightWrapped = true;\r
-\r
-\r
- public AlignViewport(AlignmentI al,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\r
-\r
- this.startRes = 0;\r
- this.endRes = al.getWidth()-1;\r
- this.startSeq = 0;\r
- this.endSeq = al.getHeight()-1;\r
- this.showText = showText;\r
- this.showBoxes = showBoxes;\r
- this.wrapAlignment = wrapAlignment;\r
-\r
- setAlignment(al);\r
- setFont( font );\r
- }\r
-\r
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\r
- }\r
-\r
- AlignmentAnnotation consensus;\r
- AlignmentAnnotation conservation;\r
- public void updateConservation()\r
- {\r
- Annotation [] annotations = new Annotation[alignment.getWidth()];\r
-\r
- Conservation cons = new jalview.analysis.Conservation("All",\r
- jalview.schemes.ResidueProperties.propHash, 3,\r
- alignment.getSequences(), 0,\r
- alignment.getWidth());\r
- cons.calculate();\r
- cons.verdict(false, 100);\r
- cons.findQuality();\r
- String sequence = cons.getConsSequence().getSequence();\r
- float minR,minG,minB, maxR,maxG,maxB;\r
- minR = 0.3f;\r
- minG = 0f;\r
- minB = 0f;\r
- maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring\r
- float min = cons.qualityRange[0].floatValue();\r
- float max = cons.qualityRange[1].floatValue();\r
-\r
- for (int i = 0; i < alignment.getWidth(); i++)\r
- {\r
- float value = 0;\r
- try\r
+ int startRes;\r
+ int endRes;\r
+ int startSeq;\r
+ int endSeq;\r
+ boolean showDBPrefix = true;\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
+ int wrappedWidth;\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
+\r
+ /** DOCUMENT ME!! */\r
+ public Vector vconsensus;\r
+ AlignmentAnnotation consensus;\r
+ AlignmentAnnotation conservation;\r
+ AlignmentAnnotation quality;\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
+\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
+ showDBPrefix = Cache.getDefault("SHOW_DBPREFIX", true);\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
+ 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 showSequenceFeatures(boolean b)\r
+ {\r
+ showSequenceFeatures = b;\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
+ 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(),\r
+ 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
+ catch (OutOfMemoryError error)\r
{\r
- //value = Integer.parseInt(sequence.charAt(i) + "");\r
- value = ((Double) cons.quality.get(i)).floatValue();\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
+ System.out.println("Conservation calculation: " + error);\r
+ System.gc();\r
+\r
}\r
- catch (Exception ex)\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, 1);\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
- if (sequence.charAt(i) == '*') value = 10;\r
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of memory calculating consensus!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ javax.swing.JOptionPane.WARNING_MESSAGE);\r
+ System.out.println("Consensus calculation: " + error);\r
+ System.gc();\r
}\r
- float vprop = value-min;\r
- vprop/=max;\r
- annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- "Conservation graph", ' ', value, new Color(minR+maxR*vprop, minB+maxB*vprop, minB+maxB*vprop));\r
+\r
}\r
\r
- if(conservation==null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceGroup getSelectionGroup()\r
{\r
- conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment",\r
- annotations,\r
- cons.qualityRange[0].floatValue(),\r
- cons.qualityRange[1].floatValue(), 1);\r
- alignment.addAnnotation(conservation);\r
+ return selectionGroup;\r
}\r
- else\r
- conservation.annotations = annotations;\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
- public void updateConsensus()\r
- {\r
- Annotation [] annotations = new Annotation[alignment.getWidth()];\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void setConservationSelected(boolean b)\r
+ {\r
+ conservationColourSelected = b;\r
+ }\r
\r
- Vector cons = alignment.getAAFrequency();\r
- Hashtable hash = null;\r
- for (int i = 0; i < alignment.getWidth(); i++)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getAbovePIDThreshold()\r
{\r
- hash = (Hashtable) cons.elementAt(i);\r
- float value = Float.parseFloat(hash.get("maxCount").toString());\r
- value /= Float.parseFloat(hash.get("size").toString());\r
+ return abovePIDThreshold;\r
+ }\r
\r
- value *= 100;\r
- String maxRes = hash.get("maxResidue")+" ";\r
- String mouseOver = hash.get("maxResidue")+" ";\r
- if(maxRes.length()>2)\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
- mouseOver = "["+maxRes+"] ";\r
- maxRes = "+ ";\r
+ seq = 0;\r
}\r
\r
- mouseOver += (int)value+"%";\r
- annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\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
- if(consensus==null)\r
- {\r
- consensus = new AlignmentAnnotation("% Identity",\r
- "PID", annotations, 0f, 100f, 1);\r
- alignment.addAnnotation(consensus);\r
- }\r
- else\r
- consensus.annotations = annotations;\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
- }\r
+ java.awt.FontMetrics fm = c.getFontMetrics(font);\r
+ setCharHeight(fm.getHeight());\r
+ setCharWidth(fm.charWidth('M'));\r
+ }\r
\r
- public String getVisibleConsensus()\r
- {\r
- return visibleConsensus;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Font getFont()\r
+ {\r
+ return font;\r
+ }\r
\r
- String visibleConsensus;\r
- Vector consensusV = new Vector();\r
- public Vector getConsensus(boolean recalculate)\r
- {\r
- if(recalculate || consensusV.size()<1)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param w DOCUMENT ME!\r
+ */\r
+ public void setCharWidth(int w)\r
{\r
- consensusV = alignment.getAAFrequency();\r
- StringBuffer sb = new StringBuffer();\r
- Hashtable hash = null;\r
- for (int i = 0; i < consensusV.size(); i++)\r
- {\r
- hash = (Hashtable) consensusV.elementAt(i);\r
- sb.append(hash.get("maxResidue").toString().charAt(0));\r
- }\r
- visibleConsensus = sb.toString();\r
- }\r
-\r
-\r
- return consensusV;\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
-\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
- return startRes;\r
- }\r
-\r
- public int getEndRes() {\r
- return endRes;\r
- }\r
-\r
- public int getStartSeq() {\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
-\r
- public void setStartRes(int res) {\r
- this.startRes = res;\r
- }\r
- public void setStartSeq(int seq) {\r
- this.startSeq = seq;\r
- }\r
- public void setEndRes(int res) {\r
- if (res > alignment.getWidth()-1) {\r
- System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
- res = alignment.getWidth() -1;\r
- }\r
- if (res < 0) {\r
- res = 0;\r
- }\r
- this.endRes = res;\r
- }\r
- public void setEndSeq(int seq) {\r
- if (seq > alignment.getHeight()) {\r
- seq = alignment.getHeight();\r
- }\r
- if (seq < 0) {\r
- seq = 0;\r
- }\r
- this.endSeq = seq;\r
- }\r
- public int getEndSeq() {\r
- return endSeq;\r
- }\r
-\r
- public void setFont(Font f) {\r
- font = f;\r
- javax.swing.JFrame temp = new javax.swing.JFrame();\r
- temp.addNotify();\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
- return font;\r
- }\r
- public void setCharWidth(int w) {\r
- this.charWidth = w;\r
- }\r
- public int getCharWidth() {\r
- return charWidth;\r
- }\r
- public void setCharHeight(int h) {\r
- this.charHeight = h;\r
- }\r
- public int getCharHeight() {\r
- return charHeight;\r
- }\r
- public void setChunkWidth(int w) {\r
- this.chunkWidth = w;\r
- }\r
- public int getChunkWidth() {\r
- return chunkWidth;\r
- }\r
- public void setChunkHeight(int h) {\r
- this.chunkHeight = h;\r
- }\r
- public int getChunkHeight() {\r
- return chunkHeight;\r
- }\r
- public AlignmentI getAlignment() {\r
- return alignment;\r
- }\r
- public void setAlignment(AlignmentI align) {\r
- this.alignment = align;\r
- }\r
-\r
- public void setWrapAlignment(boolean state) {\r
- wrapAlignment = state;\r
- }\r
- public void setShowText(boolean state) {\r
- showText = state;\r
- }\r
-\r
- public void setRenderGaps(boolean state){\r
- renderGaps = state;\r
- if(renderer instanceof SequenceRenderer)\r
- {\r
- SequenceRenderer sr = (SequenceRenderer)renderer;\r
- sr.renderGaps(state);\r
- }\r
- }\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
- showBoxes = state;\r
- }\r
-\r
- public boolean getWrapAlignment() {\r
- return wrapAlignment;\r
- }\r
- public boolean getShowText() {\r
- return showText;\r
- }\r
- public boolean getShowBoxes() {\r
- return showBoxes;\r
- }\r
-\r
- public char getGapCharacter() {\r
- return getAlignment().getGapCharacter();\r
- }\r
- public void setGapCharacter(char gap) {\r
- if (getAlignment() != null) {\r
- getAlignment().setGapCharacter(gap);\r
- }\r
- }\r
- public void setThreshold(int thresh) {\r
- threshold = thresh;\r
- }\r
- public int getThreshold() {\r
- return threshold;\r
- }\r
- public void setIncrement(int inc) {\r
- increment = inc;\r
- }\r
- public int getIncrement() {\r
- return increment;\r
- }\r
- public int getIndex(int y) {\r
- int y1 = 0;\r
- int starty = getStartSeq();\r
- int endy = getEndSeq();\r
-\r
- for (int i = starty; i <= endy; i++) {\r
- if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {\r
- int y2 = y1 + getCharHeight();\r
-\r
- if (y>=y1 && y <=y2) {\r
- return i;\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
- y1 = y2;\r
- } else {\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
- return -1;\r
- }\r
\r
- public ColumnSelection getColumnSelection() {\r
- return colSel;\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
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getShowDBPrefix()\r
+ {\r
+ return showDBPrefix;\r
+ }\r
\r
- public void resetSeqLimits(int height) {\r
- setEndSeq(height/getCharHeight());\r
- }\r
- public void setCurrentTree(NJTree tree) {\r
- currentTree = tree;\r
- }\r
- public NJTree getCurrentTree() {\r
- return currentTree;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void setShowDBPrefix(boolean b)\r
+ {\r
+ showDBPrefix = b;\r
+ }\r
\r
- public void setRenderer(RendererI rend) {\r
- this.renderer = rend;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getShowAnnotation()\r
+ {\r
+ return showAnnotation;\r
}\r
\r
- public RendererI getRenderer() {\r
- return renderer;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void setShowAnnotation(boolean b)\r
+ {\r
+ showAnnotation = b;\r
}\r
\r
- public void setColourAppliesToAllGroups(boolean b)\r
- { colourAppliesToAllGroups = b; }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getScaleAboveWrapped()\r
+ {\r
+ return scaleAboveWrapped;\r
+ }\r
\r
- public boolean getColourAppliesToAllGroups()\r
- {return colourAppliesToAllGroups; }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getScaleLeftWrapped()\r
+ {\r
+ return scaleLeftWrapped;\r
+ }\r
\r
- public boolean getShowFullId()\r
- {\r
- return showFullId;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getScaleRightWrapped()\r
+ {\r
+ return scaleRightWrapped;\r
+ }\r
\r
- public void setShowFullId(boolean b)\r
- {\r
- showFullId = b;\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
- public boolean getShowAnnotation()\r
- {\r
- return showAnnotation;\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
- public void setShowAnnotation(boolean b)\r
- {\r
- showAnnotation = b;\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
- public boolean getScaleAboveWrapped()\r
- { return scaleAboveWrapped;}\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
- public boolean getScaleLeftWrapped()\r
- { return scaleLeftWrapped; }\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
- public boolean getScaleRightWrapped()\r
- { return scaleRightWrapped; }\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 setScaleAboveWrapped(boolean b)\r
- { scaleAboveWrapped = b; }\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
- public void setScaleLeftWrapped(boolean b)\r
- { scaleLeftWrapped = b; }\r
+ }\r
\r
- public void setScaleRightWrapped(boolean b)\r
- { scaleRightWrapped = b; }\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
git://source.jalview.org / jalview.git / blobdiff