-/*\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
-\r
-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-import jalview.bin.*;\r
-import jalview.analysis.*;\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 = 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 showConsensus = 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
- 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 = true;\r
- boolean scaleLeftWrapped = true;\r
- boolean scaleRightWrapped = true;\r
-\r
- public AlignViewport(AlignmentI al, JalviewLite applet)\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
- setFont(font);\r
-\r
-\r
- if(applet!=null)\r
- {\r
- String param = applet.getParameter("showFullId");\r
- if (param != null)\r
- showFullId = Boolean.valueOf(param).booleanValue();\r
-\r
- param = applet.getParameter("showAnnotation");\r
- if (param != null)\r
- showAnnotation = Boolean.valueOf(param).booleanValue();\r
-\r
- param = applet.getParameter("showConservation");\r
- if (param != null)\r
- showConservation = Boolean.valueOf(param).booleanValue();\r
-\r
- param = applet.getParameter("showQuality");\r
- if (param != null)\r
- showQuality = Boolean.valueOf(param).booleanValue();\r
-\r
- param = applet.getParameter("showConsensus");\r
- if (param != null)\r
- showConsensus = Boolean.valueOf(param).booleanValue();\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(applet!=null && applet.getParameter("defaultColour")!=null)\r
- {\r
- globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
- applet.getParameter("defaultColour"));\r
- if(globalColourScheme!=null)\r
- globalColourScheme.setConsensus( vconsensus );\r
- }\r
- }\r
-\r
-\r
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\r
- }\r
-\r
- public Vector vconsensus;\r
- AlignmentAnnotation consensus;\r
- AlignmentAnnotation conservation;\r
- AlignmentAnnotation quality;\r
-\r
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
-\r
- public void updateConservation()\r
- {\r
- Conservation cons = new jalview.analysis.Conservation("All",\r
- jalview.schemes.ResidueProperties.propHash, 3,\r
- alignment.getSequences(), 0,\r
- alignment.getWidth()-1);\r
- cons.calculate();\r
- cons.verdict(false, ConsPercGaps);\r
- cons.findQuality();\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,minG,minB, maxR,maxG,maxB;\r
- minR = 0.3f;\r
- minG = 0.0f;\r
- minB = 0f;\r
- maxR = 1.0f-minR; maxG=0.9f-minG; maxB=0f-minB; // scalable range for colouring both Conservation and Quality\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
- try\r
- {\r
- value = Integer.parseInt(sequence.charAt(i) + "");\r
- }\r
- catch (Exception ex)\r
- {\r
- if (sequence.charAt(i) == '*') value = 11;\r
- if (sequence.charAt(i) == '+') value = 10;\r
- }\r
- float vprop = value-min;\r
- vprop/=max;\r
-\r
- annotations[i] = new Annotation(sequence.charAt(i) + "",\r
- "", ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
- // Quality calc\r
- value = ((Double) cons.quality.elementAt(i)).floatValue();\r
- vprop = value - qmin;\r
- vprop/=qmax;\r
- qannotations[i] = new Annotation(" ",\r
- String.valueOf(value), ' ', value, new Color(minR+maxR*vprop, minG+maxG*vprop, minB+maxB*vprop));\r
- }\r
-\r
- if(conservation==null)\r
- {\r
- conservation = new AlignmentAnnotation("Conservation",\r
- "Conservation of total alignment less than "+ConsPercGaps+"% gaps",\r
- annotations,\r
- 0f, // cons.qualityRange[0].floatValue(),\r
- 11f, // cons.qualityRange[1].floatValue()\r
- 1);\r
- if(showConservation)\r
- alignment.addAnnotation(conservation);\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
- if(showQuality)\r
- alignment.addAnnotation(quality);\r
- }\r
- else {\r
- conservation.annotations = annotations;\r
- quality.annotations = qannotations;\r
- quality.graphMax = cons.qualityRange[1].floatValue();\r
- }\r
-\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
- vconsensus = alignment.getAAFrequency();\r
- else\r
- {\r
- Vector temp = alignment.getAAFrequency();\r
- vconsensus.removeAllElements();\r
- Enumeration e = temp.elements();\r
- while(e.hasMoreElements())\r
- {\r
- vconsensus.addElement(e.nextElement());\r
- }\r
- }\r
- Hashtable hash = null;\r
- for (int i = 0; i<alignment.getWidth(); i++)\r
- {\r
- hash = (Hashtable) vconsensus.elementAt(i);\r
- float value = new Float(hash.get("maxCount").toString()).floatValue();\r
- value /= new Float(hash.get("size").toString()).floatValue();\r
-\r
- value *= 100;\r
- String maxRes = hash.get("maxResidue")+" ";\r
- String mouseOver = hash.get("maxResidue")+" ";\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
-\r
- if(consensus==null)\r
- {\r
- consensus = new AlignmentAnnotation("Consensus",\r
- "PID", annotations, 0f, 100f, 1);\r
- if(showConsensus)\r
- alignment.addAnnotation(consensus);\r
- }\r
- else\r
- consensus.annotations = annotations;\r
-\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
- // log.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
- java.awt.Frame temp = new java.awt.Frame();\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
- }\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
- }\r
- y1 = y2;\r
- } else {\r
- return -1;\r
- }\r
- }\r
- return -1;\r
- }\r
-\r
- public ColumnSelection getColumnSelection() {\r
- return colSel;\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
-\r
- public void setColourAppliesToAllGroups(boolean b)\r
- { colourAppliesToAllGroups = b; }\r
-\r
- public boolean getColourAppliesToAllGroups()\r
- {return colourAppliesToAllGroups; }\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
- { return scaleAboveWrapped;}\r
-\r
- public boolean getScaleLeftWrapped()\r
- { return scaleLeftWrapped; }\r
-\r
- public boolean getScaleRightWrapped()\r
- { return scaleRightWrapped; }\r
-\r
- public void setScaleAboveWrapped(boolean b)\r
- { scaleAboveWrapped = b; }\r
-\r
- public void setScaleLeftWrapped(boolean b)\r
- { scaleLeftWrapped = b; }\r
-\r
- public void setScaleRightWrapped(boolean b)\r
- { scaleRightWrapped = b; }\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+
+import jalview.analysis.*;
+import jalview.api.AlignViewportI;
+import jalview.bin.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.VamsasSource;
+import jalview.viewmodel.AlignmentViewport;
+
+public class AlignViewport extends AlignmentViewport implements
+ AlignViewportI, SelectionSource, VamsasSource
+{
+ int startRes;
+
+ int endRes;
+
+ int startSeq;
+
+ int endSeq;
+
+ boolean cursorMode = false;
+
+ 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 upperCasebold = false;
+
+ int charHeight;
+
+ int charWidth;
+
+ int wrappedWidth;
+
+ Font font = new Font("SansSerif", Font.PLAIN, 10);
+
+ boolean validCharWidth = true;
+
+ int threshold;
+
+ int increment;
+
+ NJTree currentTree = null;
+
+ boolean scaleAboveWrapped = true;
+
+ boolean scaleLeftWrapped = true;
+
+ boolean scaleRightWrapped = true;
+
+ // The following vector holds the features which are
+ // currently visible, in the correct order or rendering
+ public Hashtable featuresDisplayed;
+
+ boolean showHiddenMarkers = true;
+
+ public jalview.bin.JalviewLite applet;
+
+ Hashtable sequenceColours;
+
+ boolean MAC = false;
+
+ Stack historyList = new Stack();
+
+ Stack redoList = new Stack();
+
+ public void finalize()
+ {
+ applet = null;
+ quality = null;
+ alignment = null;
+ colSel = null;
+ }
+
+ public AlignViewport(AlignmentI al, JalviewLite applet)
+ {
+ calculator = new jalview.workers.AlignCalcManager();
+ this.applet = applet;
+ setAlignment(al);
+ // we always pad gaps
+ this.setPadGaps(true);
+ this.startRes = 0;
+ this.endRes = al.getWidth() - 1;
+ this.startSeq = 0;
+ this.endSeq = al.getHeight() - 1;
+ if (applet != null)
+ {
+ // get the width and height scaling factors if they were specified
+ String param = applet.getParameter("widthScale");
+ if (param != null)
+ {
+ try
+ {
+ widthScale = new Float(param).floatValue();
+ } catch (Exception e)
+ {
+ }
+ if (widthScale <= 1.0)
+ {
+ System.err
+ .println("Invalid alignment character width scaling factor ("
+ + widthScale + "). Ignoring.");
+ widthScale = 1;
+ }
+ if (applet.debug)
+ {
+ System.err
+ .println("Alignment character width scaling factor is now "
+ + widthScale);
+ }
+ }
+ param = applet.getParameter("heightScale");
+ if (param != null)
+ {
+ try
+ {
+ heightScale = new Float(param).floatValue();
+ } catch (Exception e)
+ {
+ }
+ if (heightScale <= 1.0)
+ {
+ System.err
+ .println("Invalid alignment character height scaling factor ("
+ + heightScale + "). Ignoring.");
+ heightScale = 1;
+ }
+ if (applet.debug)
+ {
+ System.err
+ .println("Alignment character height scaling factor is now "
+ + heightScale);
+ }
+ }
+ }
+ setFont(font);
+
+ MAC = new jalview.util.Platform().isAMac();
+
+ if (applet != null)
+ {
+ showJVSuffix = applet.getDefaultParameter("showFullId", showJVSuffix);
+
+ showAnnotation = applet.getDefaultParameter("showAnnotation",
+ showAnnotation);
+
+ showConservation = applet.getDefaultParameter("showConservation",
+ showConservation);
+
+ showQuality = applet.getDefaultParameter("showQuality", showQuality);
+
+ showConsensus = applet.getDefaultParameter("showConsensus",
+ showConsensus);
+
+ showUnconserved = applet.getDefaultParameter("showUnconserved",
+ showUnconserved);
+
+ String param = applet.getParameter("upperCase");
+ if (param != null)
+ {
+ if (param.equalsIgnoreCase("bold"))
+ {
+ upperCasebold = true;
+ }
+ }
+ sortByTree = applet.getDefaultParameter("sortByTree", sortByTree);
+
+ followHighlight = applet.getDefaultParameter("automaticScrolling",
+ followHighlight);
+ followSelection = followHighlight;
+
+ showSequenceLogo = applet.getDefaultParameter("showSequenceLogo",
+ showSequenceLogo);
+
+ normaliseSequenceLogo = applet.getDefaultParameter(
+ "normaliseSequenceLogo", applet.getDefaultParameter(
+ "normaliseLogo", normaliseSequenceLogo));
+
+ showGroupConsensus = applet.getDefaultParameter("showGroupConsensus",
+ showGroupConsensus);
+
+ showGroupConservation = applet.getDefaultParameter(
+ "showGroupConservation", showGroupConservation);
+
+ showConsensusHistogram = applet.getDefaultParameter(
+ "showConsensusHistogram", showConsensusHistogram);
+
+ }
+
+ if (applet != null)
+ {
+ String colour = applet.getParameter("defaultColour");
+
+ if (colour == null)
+ {
+ colour = applet.getParameter("userDefinedColour");
+ if (colour != null)
+ {
+ colour = "User Defined";
+ }
+ }
+
+ if (colour != null)
+ {
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,
+ colour);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setConsensus(hconsensus);
+ }
+ }
+
+ if (applet.getParameter("userDefinedColour") != null)
+ {
+ ((UserColourScheme) globalColourScheme).parseAppletParameter(applet
+ .getParameter("userDefinedColour"));
+ }
+ }
+ initAutoAnnotation();
+
+ }
+
+ public void showSequenceFeatures(boolean b)
+ {
+ showSequenceFeatures = b;
+ }
+
+ public boolean getShowSequenceFeatures()
+ {
+ return showSequenceFeatures;
+ }
+
+ /**
+ * 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;
+ }
+
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ public int getStartSeq()
+ {
+ return startSeq;
+ }
+
+ public void setStartRes(int res)
+ {
+ this.startRes = res;
+ }
+
+ public void setStartSeq(int seq)
+ {
+ this.startSeq = seq;
+ }
+
+ 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;
+ }
+
+ public void setEndSeq(int seq)
+ {
+ if (seq > alignment.getHeight())
+ {
+ seq = alignment.getHeight();
+ }
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+ this.endSeq = seq;
+ }
+
+ public int getEndSeq()
+ {
+ return endSeq;
+ }
+
+ java.awt.Frame nullFrame;
+
+ protected FeatureSettings featureSettings = null;
+
+ private float heightScale = 1, widthScale = 1;
+
+ public void setFont(Font f)
+ {
+ font = f;
+ if (nullFrame == null)
+ {
+ nullFrame = new java.awt.Frame();
+ nullFrame.addNotify();
+ }
+
+ java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
+ setCharHeight((int) (heightScale * fm.getHeight()));
+ charWidth = (int) (widthScale * fm.charWidth('M'));
+
+ if (upperCasebold)
+ {
+ Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
+ fm = nullFrame.getGraphics().getFontMetrics(f2);
+ charWidth = (int) (widthScale * (fm.stringWidth("MMMMMMMMMMM") / 10));
+ }
+ }
+
+ public Font getFont()
+ {
+ return font;
+ }
+
+ public int getCharWidth()
+ {
+ return charWidth;
+ }
+
+ public void setCharHeight(int h)
+ {
+ this.charHeight = h;
+ }
+
+ public int getCharHeight()
+ {
+ return charHeight;
+ }
+
+ public void setWrappedWidth(int w)
+ {
+ this.wrappedWidth = w;
+ }
+
+ public int getwrappedWidth()
+ {
+ return wrappedWidth;
+ }
+
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ public void setAlignment(AlignmentI align)
+ {
+ this.alignment = align;
+ }
+
+ public void setWrapAlignment(boolean state)
+ {
+ wrapAlignment = state;
+ }
+
+ public void setShowText(boolean state)
+ {
+ showText = state;
+ }
+
+ public void setRenderGaps(boolean state)
+ {
+ renderGaps = state;
+ }
+
+ public boolean getColourText()
+ {
+ return showColourText;
+ }
+
+ public void setColourText(boolean state)
+ {
+ showColourText = state;
+ }
+
+ public void setShowBoxes(boolean state)
+ {
+ showBoxes = state;
+ }
+
+ public boolean getWrapAlignment()
+ {
+ return wrapAlignment;
+ }
+
+ public boolean getShowText()
+ {
+ return showText;
+ }
+
+ public boolean getShowBoxes()
+ {
+ return showBoxes;
+ }
+
+ public char getGapCharacter()
+ {
+ return getAlignment().getGapCharacter();
+ }
+
+ public void setGapCharacter(char gap)
+ {
+ if (getAlignment() != null)
+ {
+ getAlignment().setGapCharacter(gap);
+ }
+ }
+
+ public void setThreshold(int thresh)
+ {
+ threshold = thresh;
+ }
+
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ public void setIncrement(int inc)
+ {
+ increment = inc;
+ }
+
+ public int getIncrement()
+ {
+ return increment;
+ }
+
+ public void resetSeqLimits(int height)
+ {
+ setEndSeq(height / getCharHeight());
+ }
+
+ public void setCurrentTree(NJTree tree)
+ {
+ currentTree = tree;
+ }
+
+ public NJTree getCurrentTree()
+ {
+ return currentTree;
+ }
+
+ public boolean getShowJVSuffix()
+ {
+ return showJVSuffix;
+ }
+
+ public void setShowJVSuffix(boolean b)
+ {
+ showJVSuffix = b;
+ }
+
+ public boolean getShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ public void setShowAnnotation(boolean b)
+ {
+ showAnnotation = b;
+ }
+
+ public boolean getScaleAboveWrapped()
+ {
+ return scaleAboveWrapped;
+ }
+
+ public boolean getScaleLeftWrapped()
+ {
+ return scaleLeftWrapped;
+ }
+
+ public boolean getScaleRightWrapped()
+ {
+ return scaleRightWrapped;
+ }
+
+ public void setScaleAboveWrapped(boolean b)
+ {
+ scaleAboveWrapped = b;
+ }
+
+ public void setScaleLeftWrapped(boolean b)
+ {
+ scaleLeftWrapped = b;
+ }
+
+ public void setScaleRightWrapped(boolean b)
+ {
+ scaleRightWrapped = b;
+ }
+
+ public void setIgnoreGapsConsensus(boolean b)
+ {
+ ignoreGapsInConsensusCalculation = b;
+ updateConsensus(null);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ ignoreGapsInConsensusCalculation);
+
+ }
+ }
+
+ public boolean getShowHiddenMarkers()
+ {
+ return showHiddenMarkers;
+ }
+
+ public void setShowHiddenMarkers(boolean show)
+ {
+ showHiddenMarkers = show;
+ }
+
+ 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);
+ }
+ }
+
+ boolean centreColumnLabels;
+
+ public boolean getCentreColumnLabels()
+ {
+ return centreColumnLabels;
+ }
+
+ public void updateSequenceIdColours()
+ {
+
+ for (SequenceGroup sg : alignment.getGroups())
+ {
+ if (sg.idColour != null)
+ {
+ for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
+ {
+ this.setSequenceColour(s, sg.idColour);
+ }
+ }
+ }
+ }
+
+ public boolean followHighlight = true;
+
+ public boolean getFollowHighlight()
+ {
+ return followHighlight;
+ }
+
+ public boolean followSelection = true;
+
+ /**
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
+ */
+ public boolean getFollowSelection()
+ {
+ return followSelection;
+ }
+
+ public void sendSelection()
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(applet).sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
+ }
+
+ /**
+ * synthesize a column selection if none exists so it covers the given
+ * selection group. if wholewidth is false, no column selection is made if the
+ * selection group covers the whole alignment width.
+ *
+ * @param sg
+ * @param wholewidth
+ */
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+ {
+ int sgs, sge;
+ if (sg != null
+ && (sgs = sg.getStartRes()) >= 0
+ && sg.getStartRes() <= (sge = sg.getEndRes())
+ && (colSel == null || colSel.getSelected() == null || colSel
+ .getSelected().size() == 0))
+ {
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+ {
+ // do nothing
+ return;
+ }
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
+ }
+ }
+ }
+
+ @Override
+ public boolean hasHiddenColumns()
+ {
+ return hasHiddenColumns;
+ }
+
+ public boolean isNormaliseSequenceLogo()
+ {
+ return normaliseSequenceLogo;
+ }
+
+ public void setNormaliseSequenceLogo(boolean state)
+ {
+ normaliseSequenceLogo = state;
+ }
+
+ /**
+ *
+ * @return true if alignment characters should be displayed
+ */
+ public boolean isValidCharWidth()
+ {
+ return validCharWidth;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff