+/*\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
-import jalview.io.*;\r
-import jalview.analysis.NJTree;\r
+\r
+import jalview.analysis.*;\r
+import jalview.bin.*;\r
import jalview.datamodel.*;\r
import jalview.schemes.*;\r
-import java.util.*;\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 showText = true;\r
+ boolean showColourText = false;\r
+ boolean showBoxes = true;\r
+ boolean wrapAlignment = false;\r
boolean renderGaps = true;\r
boolean showSequenceFeatures = false;\r
-\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
-\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
- RendererI renderer = new SequenceRenderer(this);\r
+ updateFromPreferences();\r
+ }\r
\r
- int charHeight;\r
- int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\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
- Font font = new Font("SansSerif",Font.PLAIN,10);\r
- AlignmentI alignment;\r
+ if (fontStyle.equals("bold"))\r
+ {\r
+ style = 1;\r
+ }\r
+ else if (fontStyle.equals("italic"))\r
+ {\r
+ style = 2;\r
+ }\r
\r
- ColumnSelection colSel = new ColumnSelection();\r
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)));\r
+ }\r
+ else\r
+ {\r
+ setFont(font);\r
+ }\r
\r
- String visibleConsensus;\r
+ alignment.setGapCharacter(Preferences.gapSymbol);\r
\r
- int threshold;\r
- int increment;\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
- NJTree currentTree = null;\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
- public AlignViewport(AlignmentI da,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\r
- this(0,da.getWidth()-1,0,da.getHeight()-1,\r
- showText,\r
- showBoxes,\r
- wrapAlignment);\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setConsensus(vconsensus);\r
+ }\r
+ }\r
+ }\r
\r
- setAlignment(da);\r
+ public void showSequenceFeatures(boolean b)\r
+ {\r
+ showSequenceFeatures = b;\r
}\r
\r
- public AlignViewport(int startRes, int endRes,\r
- int startSeq, int endSeq,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\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
- this.startRes = startRes;\r
- this.endRes = endRes;\r
- this.startSeq = startSeq;\r
- this.endSeq = endSeq;\r
- this.showText = showText;\r
- this.showBoxes = showBoxes;\r
- this.wrapAlignment = wrapAlignment;\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
- setFont( font );\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
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\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
- public String getVisibleConsensus()\r
- {\r
- return visibleConsensus;\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
- Vector consensus = new Vector();\r
- public Vector getConsensus(boolean recalculate)\r
+ public void updateConsensus()\r
{\r
- if(recalculate || consensus.size()<1)\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
- consensus = alignment.getAAFrequency();\r
- StringBuffer sb = new StringBuffer();\r
- Hashtable hash = null;\r
- for (int i = 0; i < consensus.size(); i++)\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
- hash = (Hashtable) consensus.elementAt(i);\r
- sb.append(hash.get("maxResidue").toString().charAt(0));\r
+ vconsensus.add(e.nextElement());\r
}\r
- visibleConsensus = sb.toString();\r
}\r
\r
+ Hashtable hash = null;\r
\r
- return consensus;\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
selectionGroup = sg;\r
}\r
\r
+ public boolean getConservationSelected()\r
+ {\r
+ return conservationColourSelected;\r
+ }\r
\r
- public boolean getConservationSelected()\r
- {\r
- return conservationColourSelected;\r
- }\r
-\r
- public void setConservationSelected(boolean b)\r
- {\r
- conservationColourSelected = b;\r
- }\r
+ public void setConservationSelected(boolean b)\r
+ {\r
+ conservationColourSelected = b;\r
+ }\r
\r
- public boolean getAbovePIDThreshold()\r
- {\r
- return abovePIDThreshold;\r
- }\r
+ public boolean getAbovePIDThreshold()\r
+ {\r
+ return abovePIDThreshold;\r
+ }\r
\r
- public void setAbovePIDThreshold(boolean b)\r
- {\r
- abovePIDThreshold = b;\r
- }\r
+ public void setAbovePIDThreshold(boolean b)\r
+ {\r
+ abovePIDThreshold = b;\r
+ }\r
\r
- public int getStartRes() {\r
+ public int getStartRes()\r
+ {\r
return startRes;\r
}\r
\r
- public int getEndRes() {\r
+ public int getEndRes()\r
+ {\r
return endRes;\r
}\r
\r
- public int getStartSeq() {\r
+ public int getStartSeq()\r
+ {\r
return startSeq;\r
}\r
\r
public void setGlobalColourScheme(ColourSchemeI cs)\r
{\r
- globalColourScheme = cs;\r
+ globalColourScheme = cs;\r
}\r
\r
public ColourSchemeI getGlobalColourScheme()\r
return globalColourScheme;\r
}\r
\r
-\r
- public void setStartRes(int res) {\r
+ public void setStartRes(int res)\r
+ {\r
this.startRes = res;\r
}\r
- public void setStartSeq(int seq) {\r
+\r
+ public void setStartSeq(int seq)\r
+ {\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
+ public void setEndRes(int res)\r
+ {\r
+ if (res > (alignment.getWidth() - 1))\r
+ {\r
+ // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
+ res = alignment.getWidth() - 1;\r
}\r
- if (res < 0) {\r
+\r
+ if (res < 0)\r
+ {\r
res = 0;\r
}\r
+\r
this.endRes = res;\r
}\r
- public void setEndSeq(int seq) {\r
- if (seq > alignment.getHeight()) {\r
+\r
+ public void setEndSeq(int seq)\r
+ {\r
+ if (seq > alignment.getHeight())\r
+ {\r
seq = alignment.getHeight();\r
}\r
- if (seq < 0) {\r
+\r
+ if (seq < 0)\r
+ {\r
seq = 0;\r
}\r
+\r
this.endSeq = seq;\r
}\r
- public int getEndSeq() {\r
+\r
+ public int getEndSeq()\r
+ {\r
return endSeq;\r
}\r
\r
- public void setFont(Font f) {\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
+ public Font getFont()\r
+ {\r
return font;\r
}\r
- public void setCharWidth(int w) {\r
+\r
+ public void setCharWidth(int w)\r
+ {\r
this.charWidth = w;\r
}\r
- public int getCharWidth() {\r
+\r
+ public int getCharWidth()\r
+ {\r
return charWidth;\r
}\r
- public void setCharHeight(int h) {\r
+\r
+ public void setCharHeight(int h)\r
+ {\r
this.charHeight = h;\r
}\r
- public int getCharHeight() {\r
+\r
+ public int getCharHeight()\r
+ {\r
return charHeight;\r
}\r
- public void setChunkWidth(int w) {\r
+\r
+ public void setChunkWidth(int w)\r
+ {\r
this.chunkWidth = w;\r
}\r
- public int getChunkWidth() {\r
+\r
+ public int getChunkWidth()\r
+ {\r
return chunkWidth;\r
}\r
- public void setChunkHeight(int h) {\r
+\r
+ public void setChunkHeight(int h)\r
+ {\r
this.chunkHeight = h;\r
}\r
- public int getChunkHeight() {\r
+\r
+ public int getChunkHeight()\r
+ {\r
return chunkHeight;\r
}\r
- public AlignmentI getAlignment() {\r
+\r
+ public AlignmentI getAlignment()\r
+ {\r
return alignment;\r
}\r
- public void setAlignment(AlignmentI align) {\r
+\r
+ public void setAlignment(AlignmentI align)\r
+ {\r
this.alignment = align;\r
}\r
\r
- public void setWrapAlignment(boolean state) {\r
+ public void setWrapAlignment(boolean state)\r
+ {\r
wrapAlignment = state;\r
}\r
- public void setShowText(boolean state) {\r
+\r
+ public void setShowText(boolean state)\r
+ {\r
showText = state;\r
}\r
\r
- public void setRenderGaps(boolean state){\r
+ public void setRenderGaps(boolean state)\r
+ {\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
showColourText = state;\r
}\r
\r
- public void setShowBoxes(boolean state) {\r
+ public void setShowBoxes(boolean state)\r
+ {\r
showBoxes = state;\r
}\r
\r
- public boolean getWrapAlignment() {\r
- return wrapAlignment;\r
+ public boolean getWrapAlignment()\r
+ {\r
+ return wrapAlignment;\r
}\r
- public boolean getShowText() {\r
+\r
+ public boolean getShowText()\r
+ {\r
return showText;\r
}\r
- public boolean getShowBoxes() {\r
+\r
+ public boolean getShowBoxes()\r
+ {\r
return showBoxes;\r
}\r
\r
- public char getGapCharacter() {\r
+ public char getGapCharacter()\r
+ {\r
return getAlignment().getGapCharacter();\r
}\r
- public void setGapCharacter(char gap) {\r
- if (getAlignment() != null) {\r
+\r
+ public void setGapCharacter(char gap)\r
+ {\r
+ if (getAlignment() != null)\r
+ {\r
getAlignment().setGapCharacter(gap);\r
}\r
}\r
- public void setThreshold(int thresh) {\r
+\r
+ public void setThreshold(int thresh)\r
+ {\r
threshold = thresh;\r
}\r
- public int getThreshold() {\r
+\r
+ public int getThreshold()\r
+ {\r
return threshold;\r
}\r
- public void setIncrement(int inc) {\r
+\r
+ public void setIncrement(int inc)\r
+ {\r
increment = inc;\r
}\r
- public int getIncrement() {\r
+\r
+ public int getIncrement()\r
+ {\r
return increment;\r
}\r
- public int getIndex(int y) {\r
- int y1 = 0;\r
+\r
+ public int getIndex(int y)\r
+ {\r
+ int y1 = 0;\r
int starty = getStartSeq();\r
- int endy = getEndSeq();\r
+ int endy = getEndSeq();\r
\r
- for (int i = starty; i <= endy; i++) {\r
- if (i < alignment.getHeight() && alignment.getSequenceAt(i) != null) {\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
+ if ( (y >= y1) && (y <= y2))\r
+ {\r
return i;\r
}\r
- y1 = y2;\r
- } else {\r
+\r
+ y1 = y2;\r
+ }\r
+ else\r
+ {\r
return -1;\r
}\r
}\r
+\r
return -1;\r
}\r
\r
- public ColumnSelection getColumnSelection() {\r
+ public ColumnSelection getColumnSelection()\r
+ {\r
return colSel;\r
}\r
\r
- public void resetSeqLimits(int height) {\r
- setEndSeq(height/getCharHeight());\r
+ public void resetSeqLimits(int height)\r
+ {\r
+ setEndSeq(height / getCharHeight());\r
}\r
- public void setCurrentTree(NJTree tree) {\r
- currentTree = tree;\r
+\r
+ public void setCurrentTree(NJTree tree)\r
+ {\r
+ currentTree = tree;\r
}\r
- public NJTree getCurrentTree() {\r
+\r
+ public NJTree getCurrentTree()\r
+ {\r
return currentTree;\r
}\r
\r
- public void setRenderer(RendererI rend) {\r
- this.renderer = rend;\r
- }\r
-\r
- public RendererI getRenderer() {\r
- return renderer;\r
- }\r
-\r
public void setColourAppliesToAllGroups(boolean b)\r
- { colourAppliesToAllGroups = b; }\r
+ {\r
+ colourAppliesToAllGroups = b;\r
+ }\r
\r
public boolean getColourAppliesToAllGroups()\r
- {return colourAppliesToAllGroups; }\r
+ {\r
+ return colourAppliesToAllGroups;\r
+ }\r
\r
public boolean getShowFullId()\r
{\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
git://source.jalview.org / jalview.git / blobdiff