X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=6b02022c61ac1ec1b9bc33577e0200889da48b7a;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=a936dac86b2fc4245f3c10a297a406600a4c4ed4;hpb=b5fdf35e68eea0a0710cae2178020645ac17e6af;p=jalview.git
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index a936dac..6b02022 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,870 +1,1797 @@
-/*
- * 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.io;
-
-import java.io.*;
-import java.net.*;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-
-public class AnnotationFile
-{
- StringBuffer text = new StringBuffer(
- "JALVIEW_ANNOTATION\n"
- + "# Created: "
- + new java.util.Date() + "\n\n");
-
- public String printAnnotations(AlignmentAnnotation[] annotations,
- Vector groups,
- Hashtable properties)
- {
- if (annotations != null)
- {
- AlignmentAnnotation row;
- String comma;
- SequenceI refSeq = null;
-
- StringBuffer colours = new StringBuffer();
- StringBuffer graphLine = new StringBuffer();
-
- Hashtable graphGroup = new Hashtable();
-
- java.awt.Color color;
-
- for (int i = 0; i < annotations.length; i++)
- {
- row = annotations[i];
-
- if (!row.visible)
- {
- continue;
- }
-
- color = null;
-
- if (row.sequenceRef == null)
- {
- if (refSeq != null)
- {
- text.append("\nSEQUENCE_REF\tALIGNMENT\n");
- }
-
- refSeq = null;
- }
-
- else if (refSeq == null || refSeq != row.sequenceRef)
- {
- refSeq = row.sequenceRef;
- text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
- }
-
- if (row.graph == AlignmentAnnotation.NO_GRAPH)
- {
- text.append("NO_GRAPH\t");
- }
- else
- {
- if (row.graph == AlignmentAnnotation.BAR_GRAPH)
- {
- text.append("BAR_GRAPH\t");
- }
- else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
- {
- text.append("LINE_GRAPH\t");
- }
-
- if (row.getThreshold() != null)
- {
- graphLine.append("GRAPHLINE\t"
- + row.label + "\t"
- + row.getThreshold().value + "\t"
- + row.getThreshold().label + "\t"
- + jalview.util.Format.getHexString(
- row.getThreshold().colour) + "\n"
- );
- }
-
- if (row.graphGroup > -1)
- {
- String key = String.valueOf(row.graphGroup);
- if (graphGroup.containsKey(key))
- {
- graphGroup.put(key, graphGroup.get(key)
- + "\t" + row.label);
- }
- else
- {
- graphGroup.put(key, row.label);
- }
- }
- }
-
- text.append(row.label + "\t");
- if (row.description != null)
- {
- text.append(row.description + "\t");
- }
-
- for (int j = 0; j < row.annotations.length; j++)
- {
- if (refSeq != null &&
- jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
- {
- continue;
- }
-
- if (row.annotations[j] != null)
- {
- comma = "";
- if (row.annotations[j].secondaryStructure != ' ')
- {
- text.append(comma + row.annotations[j].secondaryStructure);
- comma = ",";
- }
- if (row.annotations[j].displayCharacter!=null
- && row.annotations[j].displayCharacter.length() > 0
- && !row.annotations[j].displayCharacter.equals(" "))
- {
- text.append(comma + row.annotations[j].displayCharacter);
- comma = ",";
- }
-
- if (row.annotations[j] != null)
- {
- color = row.annotations[j].colour;
- if (row.annotations[j].value != 0f)
- {
- text.append(comma + row.annotations[j].value);
- }
- }
-
- if(row.annotations[j].colour!=null
- && row.annotations[j].colour!=java.awt.Color.black)
- {
- text.append(comma+"["+
- jalview.util.Format.getHexString(
- row.annotations[j].colour)+"]");
- }
- }
- text.append("|");
- }
-
- if(!Float.isNaN(row.score))
- text.append("\t"+row.score);
-
- text.append("\n");
-
- if (color != null && color != java.awt.Color.black)
- {
- colours.append("COLOUR\t"
- + row.label + "\t"
- + jalview.util.Format.getHexString(color) + "\n");
- }
-
- }
-
- text.append("\n");
-
- text.append(colours.toString());
- text.append(graphLine.toString());
- if (graphGroup.size() > 0)
- {
- text.append("COMBINE\t");
- Enumeration en = graphGroup.elements();
- while (en.hasMoreElements())
- {
- text.append(en.nextElement() + "\n");
- }
- }
- }
-
- if (groups != null)
- {
- printGroups(groups);
- }
-
- if(properties!=null)
- {
- text.append("\n\nALIGNMENT");
- Enumeration en = properties.keys();
- while(en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- text.append("\t"+key+"="+properties.get(key));
- }
-
- }
-
- return text.toString();
- }
-
- public void printGroups(Vector sequenceGroups)
- {
- SequenceGroup sg;
- for (int i = 0; i < sequenceGroups.size(); i++)
- {
- sg = (SequenceGroup) sequenceGroups.elementAt(i);
- text.append("SEQUENCE_GROUP\t"
- + sg.getName() + "\t"
- + (sg.getStartRes() + 1) + "\t"
- + (sg.getEndRes() + 1) + "\t" + "-1\t");
- for (int s = 0; s < sg.getSize(); s++)
- {
- text.append(sg.getSequenceAt(s).getName() + "\t");
- }
-
- text.append("\nPROPERTIES\t" + sg.getName() + "\t");
-
- if (sg.getDescription() != null)
- {
- text.append("description=" + sg.getDescription() + "\t");
- }
- if (sg.cs != null)
- {
- text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs) +
- "\t");
- if (sg.cs.getThreshold() != 0)
- {
- text.append("pidThreshold=" + sg.cs.getThreshold());
- }
- if (sg.cs.conservationApplied())
- {
- text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");
- }
- }
- text.append("outlineColour=" +
- jalview.util.Format.getHexString(sg.getOutlineColour()) +
- "\t");
-
- text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");
- text.append("displayText=" + sg.getDisplayText() + "\t");
- text.append("colourText=" + sg.getColourText() + "\t");
-
- if (sg.textColour != java.awt.Color.black)
- {
- text.append("textCol1=" +
- jalview.util.Format.getHexString(sg.textColour) + "\t");
- }
- if (sg.textColour2 != java.awt.Color.white)
- {
- text.append("textCol2=" +
- jalview.util.Format.getHexString(sg.textColour2) + "\t");
- }
- if (sg.thresholdTextColour != 0)
- {
- text.append("textColThreshold=" + sg.thresholdTextColour);
- }
-
- text.append("\n\n");
-
- }
- }
-
- SequenceI refSeq = null;
- public boolean readAnnotationFile(AlignmentI al,
- String file,
- String protocol)
- {
- try
- {
- BufferedReader in = null;
- if (protocol.equals(AppletFormatAdapter.FILE))
- {
- in = new BufferedReader(new FileReader(file));
- }
- else if (protocol.equals(AppletFormatAdapter.URL))
- {
- URL url = new URL(file);
- in = new BufferedReader(new InputStreamReader(url.openStream()));
- }
- else if (protocol.equals(AppletFormatAdapter.PASTE))
- {
- in = new BufferedReader(new StringReader(file));
- }
- else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
- {
- java.io.InputStream is = getClass().getResourceAsStream("/" + file);
- if (is != null)
- {
- in = new BufferedReader(new java.io.InputStreamReader(is));
- }
- }
-
- String line, label, description, token;
- int graphStyle, index;
- int refSeqIndex = 1;
- int existingAnnotations = 0;
- if (al.getAlignmentAnnotation() != null)
- {
- existingAnnotations = al.getAlignmentAnnotation().length;
- }
-
- int alWidth = al.getWidth();
-
- StringTokenizer st;
- Annotation[] annotations;
- AlignmentAnnotation annotation = null;
-
- // First confirm this is an Annotation file
- boolean jvAnnotationFile = false;
- while ( (line = in.readLine()) != null)
- {
- if (line.indexOf("#") == 0)
- {
- continue;
- }
-
- if (line.indexOf("JALVIEW_ANNOTATION") > -1)
- {
- jvAnnotationFile = true;
- break;
- }
- }
-
- if (!jvAnnotationFile)
- {
- in.close();
- return false;
- }
-
- while ( (line = in.readLine()) != null)
- {
- if (line.indexOf("#") == 0
- || line.indexOf("JALVIEW_ANNOTATION") > -1
- || line.length() == 0)
- {
- continue;
- }
-
- st = new StringTokenizer(line, "\t");
- token = st.nextToken();
- if (token.equalsIgnoreCase("COLOUR"))
- {
- colourAnnotations(al, st.nextToken(), st.nextToken());
- continue;
- }
-
- else if (token.equalsIgnoreCase("COMBINE"))
- {
- combineAnnotations(al, st);
- continue;
- }
-
- else if (token.equalsIgnoreCase("GRAPHLINE"))
- {
- addLine(al, st);
- continue;
- }
-
- else if (token.equalsIgnoreCase("SEQUENCE_REF"))
- {
- refSeq = al.findName(st.nextToken());
- try
- {
- refSeqIndex = Integer.parseInt(st.nextToken());
- if (refSeqIndex < 1)
- {
- refSeqIndex = 1;
- System.out.println(
- "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
- }
- }
- catch (Exception ex)
- {
- refSeqIndex = 1;
- }
-
- continue ;
- }
-
- else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
- {
- addGroup(al, st);
- continue;
- }
-
- else if (token.equalsIgnoreCase("PROPERTIES"))
- {
- addProperties(al, st);
- continue;
- }
-
- else if( token.equalsIgnoreCase("BELOW_ALIGNMENT"))
- {
- setBelowAlignment(al, st);
- continue;
- }
- else if( token.equalsIgnoreCase("ALIGNMENT"))
- {
- addAlignmentDetails(al, st);
- continue;
- }
-
- graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
- label = st.nextToken();
-
-
- index = 0;
- annotations = new Annotation[alWidth];
- description = null;
- float score = Float.NaN;
-
- if(st.hasMoreTokens())
- {
- line = st.nextToken();
-
- if (line.indexOf("|") ==-1)
- {
- description = line;
- if (st.hasMoreTokens())
- line = st.nextToken();
- }
-
- if(st.hasMoreTokens())
- {
- //This must be the score
- score = Float.valueOf(st.nextToken()).floatValue();
- }
-
- st = new StringTokenizer(line, "|", true);
-
-
- boolean emptyColumn = true;
- boolean onlyOneElement = (st.countTokens()==1);
-
- while (st.hasMoreElements() && index < alWidth)
- {
- token = st.nextToken().trim();
-
- if(onlyOneElement)
- {
- try
- {
- score = Float.valueOf(token).floatValue();
- break;
- }
- catch(NumberFormatException ex){}
- }
-
- if (token.equals("|"))
- {
- if (emptyColumn)
- {
- index++;
- }
-
- emptyColumn = true;
- }
- else
- {
- annotations[index++] = parseAnnotation(token);
- emptyColumn = false;
- }
- }
-
- }
-
- annotation = new AlignmentAnnotation(label,
- description,
- annotations,
- 0,
- 0,
- graphStyle);
-
- annotation.score = score;
-
- if (refSeq != null)
- {
- annotation.belowAlignment=false;
- annotation.createSequenceMapping(refSeq, refSeqIndex, false);
- annotation.adjustForAlignment();
- refSeq.addAlignmentAnnotation(annotation);
- }
-
- al.addAnnotation(annotation);
-
- al.setAnnotationIndex(annotation,
- al.getAlignmentAnnotation().length - existingAnnotations -
- 1);
- }
-
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- System.out.println("Problem reading annotation file: " + ex);
- return false;
- }
- return true;
- }
-
- Annotation parseAnnotation(String string)
- {
- String desc = null, displayChar = null;
- char ss = ' '; // secondaryStructure
- float value = 0;
- boolean parsedValue = false;
-
- //find colour here
- java.awt.Color colour = null;
- int i=string.indexOf("[");
- int j=string.indexOf("]");
- if(i>-1 && j>-1)
- {
- UserColourScheme ucs = new UserColourScheme();
-
- colour = ucs.getColourFromString(string.substring(i+1,j));
-
- string = string.substring(0,i)+string.substring(j+1);
- }
-
- StringTokenizer st = new StringTokenizer(string, ",");
- String token;
- while (st.hasMoreTokens())
- {
- token = st.nextToken().trim();
- if (token.length() == 0)
- {
- continue;
- }
-
- if (!parsedValue)
- {
- try
- {
- displayChar = token;
- value = new Float(token).floatValue();
- parsedValue = true;
- continue;
- }
- catch (NumberFormatException ex)
- {}
- }
-
- if (token.equals("H") || token.equals("E"))
- {
- // Either this character represents a helix or sheet
- // or an integer which can be displayed
- ss = token.charAt(0);
- if (displayChar.equals(token.substring(0, 1)))
- {
- displayChar = "";
- }
- }
- else if (desc == null)
- {
- desc = token;
- }
-
- }
-
- if (displayChar.length() > 1
- && desc!=null
- && desc.length() == 1)
- {
- String tmp = displayChar;
- displayChar = desc;
- desc = tmp;
- }
-
- Annotation anot = new Annotation(displayChar, desc, ss, value);
-
- anot.colour = colour;
-
- return anot;
- }
-
- void colourAnnotations(AlignmentI al, String label, String colour)
- {
- UserColourScheme ucs = new UserColourScheme(colour);
- Annotation[] annotations;
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
- {
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))
- {
- annotations = al.getAlignmentAnnotation()[i].annotations;
- for (int j = 0; j < annotations.length; j++)
- {
- if (annotations[j] != null)
- {
- annotations[j].colour = ucs.findColour('A');
- }
- }
- }
- }
- }
-
- void combineAnnotations(AlignmentI al, StringTokenizer st)
- {
- int graphGroup = -1;
- String group = st.nextToken();
- //First make sure we are not overwriting the graphIndex
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
- {
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
- {
- graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;
- al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
- break;
- }
- }
-
- //Now update groups
- while (st.hasMoreTokens())
- {
- group = st.nextToken();
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
- {
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
- {
- al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
- break;
- }
- }
- }
- }
-
- void addLine(AlignmentI al, StringTokenizer st)
- {
- String group = st.nextToken();
- AlignmentAnnotation annotation = null;
-
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
- {
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
- {
- annotation = al.getAlignmentAnnotation()[i];
- break;
- }
- }
-
- if (annotation == null)
- {
- return;
- }
- float value = new Float(st.nextToken()).floatValue();
- String label = st.hasMoreTokens() ? st.nextToken() : null;
- java.awt.Color colour = null;
- if (st.hasMoreTokens())
- {
- UserColourScheme ucs = new UserColourScheme(st.nextToken());
- colour = ucs.findColour('A');
- }
-
- annotation.setThreshold(new GraphLine(value, label, colour));
- }
-
- void addGroup(AlignmentI al, StringTokenizer st)
- {
- SequenceGroup sg = new SequenceGroup();
- sg.setName(st.nextToken());
- sg.setStartRes(Integer.parseInt(st.nextToken()) - 1);
- sg.setEndRes(Integer.parseInt(st.nextToken()) - 1);
-
- String index = st.nextToken();
- if (index.equals("-1"))
- {
- while (st.hasMoreElements())
- {
- sg.addSequence(al.findName(st.nextToken()), false);
- }
- }
- else
- {
- StringTokenizer st2 = new StringTokenizer(index, ",");
-
- while (st2.hasMoreTokens())
- {
- String tmp = st2.nextToken();
- if (tmp.equals("*"))
- {
- for (int i = 0; i < al.getHeight(); i++)
- {
- sg.addSequence(al.getSequenceAt(i), false);
- }
- }
- else if (tmp.indexOf("-") >= 0)
- {
- StringTokenizer st3 = new StringTokenizer(tmp, "-");
-
- int start = (Integer.parseInt(st3.nextToken()));
- int end = (Integer.parseInt(st3.nextToken()));
-
- if (end > start)
- {
- for (int i = start; i <= end; i++)
- {
- sg.addSequence(al.getSequenceAt(i - 1), false);
- }
- }
- }
- else
- {
- sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
- }
- }
- }
-
-
-
- if (refSeq != null)
- {
- sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);
- sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);
- }
-
- if (sg.getSize() > 0)
- {
- al.addGroup(sg);
- }
- }
-
- void addProperties(AlignmentI al, StringTokenizer st)
- {
-
- //So far we have only added groups to the annotationHash,
- //the idea is in the future properties can be added to
- //alignments, other annotations etc
- if (al.getGroups() == null)
- {
- return;
- }
- SequenceGroup sg = null;
-
- String name = st.nextToken();
-
- Vector groups = al.getGroups();
- for (int i = 0; i < groups.size(); i++)
- {
- sg = (SequenceGroup) groups.elementAt(i);
- if (sg.getName().equals(name))
- {
- break;
- }
- else
- {
- sg = null;
- }
- }
-
- if (sg != null)
- {
- String keyValue, key, value;
- while (st.hasMoreTokens())
- {
- keyValue = st.nextToken();
- key = keyValue.substring(0, keyValue.indexOf("="));
- value = keyValue.substring(keyValue.indexOf("=") + 1);
-
- if (key.equalsIgnoreCase("description"))
- {
- sg.setDescription(value);
- }
- else if (key.equalsIgnoreCase("colour"))
- {
- sg.cs = ColourSchemeProperty.getColour(al, value);
- }
- else if (key.equalsIgnoreCase("pidThreshold"))
- {
- sg.cs.setThreshold(Integer.parseInt(value), true);
-
- }
- else if (key.equalsIgnoreCase("consThreshold"))
- {
- sg.cs.setConservationInc(Integer.parseInt(value));
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(null),
- sg.getStartRes(),
- sg.getEndRes() + 1);
-
- c.calculate();
- c.verdict(false, 25);
-
- sg.cs.setConservation(c);
-
- }
- else if (key.equalsIgnoreCase("outlineColour"))
- {
- sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
- }
- else if (key.equalsIgnoreCase("displayBoxes"))
- {
- sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());
- }
- else if (key.equalsIgnoreCase("displayText"))
- {
- sg.setDisplayText(Boolean.valueOf(value).booleanValue());
- }
- else if (key.equalsIgnoreCase("colourText"))
- {
- sg.setColourText(Boolean.valueOf(value).booleanValue());
- }
- else if (key.equalsIgnoreCase("textCol1"))
- {
- sg.textColour = new UserColourScheme(value).findColour('A');
- }
- else if (key.equalsIgnoreCase("textCol2"))
- {
- sg.textColour2 = new UserColourScheme(value).findColour('A');
- }
- else if (key.equalsIgnoreCase("textColThreshold"))
- {
- sg.thresholdTextColour = Integer.parseInt(value);
- }
-
- sg.recalcConservation();
- }
- }
- }
-
- void setBelowAlignment(AlignmentI al, StringTokenizer st)
- {
- String token;
- AlignmentAnnotation aa;
- while(st.hasMoreTokens())
- {
- token = st.nextToken();
- for(int i=0; i.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.analysis.Conservation;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.ColorUtils;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.InputStreamReader;
+import java.io.StringReader;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+public class AnnotationFile
+{
+ public AnnotationFile()
+ {
+ init();
+ }
+
+ /**
+ * character used to write newlines
+ */
+ protected String newline = System.getProperty("line.separator");
+
+ /**
+ * set new line string and reset the output buffer
+ *
+ * @param nl
+ */
+ public void setNewlineString(String nl)
+ {
+ newline = nl;
+ init();
+ }
+
+ public String getNewlineString()
+ {
+ return newline;
+ }
+
+ StringBuffer text;
+
+ private void init()
+ {
+ text = new StringBuffer("JALVIEW_ANNOTATION" + newline + "# Created: "
+ + new java.util.Date() + newline + newline);
+ refSeq = null;
+ refSeqId = null;
+ }
+
+ /**
+ * convenience method for pre-2.9 annotation files which have no view, hidden
+ * columns or hidden row keywords.
+ *
+ * @param annotations
+ * @param list
+ * @param properties
+ * @return annotation file as a string.
+ */
+ public String printAnnotations(AlignmentAnnotation[] annotations,
+ List list, Hashtable properties)
+ {
+ return printAnnotations(annotations, list, properties, null, null,
+ null);
+
+ }
+
+ /**
+ * hold all the information about a particular view definition read from or
+ * written out in an annotations file.
+ */
+ public class ViewDef
+ {
+ // TODO this class is not used - remove?
+ public final String viewname;
+
+ public final HiddenSequences hidseqs;
+
+ public final HiddenColumns hiddencols;
+
+ public final Hashtable hiddenRepSeqs;
+
+ public ViewDef(String vname, HiddenSequences hseqs, HiddenColumns hcols,
+ Hashtable hRepSeqs)
+ {
+ this.viewname = vname;
+ this.hidseqs = hseqs;
+ this.hiddencols = hcols;
+ this.hiddenRepSeqs = hRepSeqs;
+ }
+ }
+
+ /**
+ * Prepare an annotation file given a set of annotations, groups, alignment
+ * properties and views.
+ *
+ * @param annotations
+ * @param list
+ * @param properties
+ * @param views
+ * @return annotation file
+ */
+ public String printAnnotations(AlignmentAnnotation[] annotations,
+ List list, Hashtable properties, HiddenColumns cs,
+ AlignmentI al, ViewDef view)
+ {
+ if (view != null)
+ {
+ if (view.viewname != null)
+ {
+ text.append("VIEW_DEF\t" + view.viewname + "\n");
+ }
+ if (list == null)
+ {
+ // list = view.visibleGroups;
+ }
+ if (cs == null)
+ {
+ cs = view.hiddencols;
+ }
+ if (al == null)
+ {
+ // add hidden rep sequences.
+ }
+ }
+ // first target - store and restore all settings for a view.
+ if (al != null && al.hasSeqrep())
+ {
+ text.append("VIEW_SETREF\t" + al.getSeqrep().getName() + "\n");
+ }
+ if (cs != null && cs.hasHiddenColumns())
+ {
+ text.append("VIEW_HIDECOLS\t");
+
+ String regions = cs.regionsToString(",", "-");
+ text.append(regions);
+ text.append("\n");
+ }
+ // TODO: allow efficient recovery of annotation data shown in several
+ // different views
+ if (annotations != null)
+ {
+ boolean oneColour = true;
+ AlignmentAnnotation row;
+ String comma;
+ SequenceI refSeq = null;
+ SequenceGroup refGroup = null;
+
+ StringBuffer colours = new StringBuffer();
+ StringBuffer graphLine = new StringBuffer();
+ StringBuffer rowprops = new StringBuffer();
+ Hashtable graphGroup = new Hashtable<>();
+ Hashtable graphGroup_refs = new Hashtable<>();
+ BitSet graphGroupSeen = new BitSet();
+
+ java.awt.Color color;
+
+ for (int i = 0; i < annotations.length; i++)
+ {
+ row = annotations[i];
+
+ if (!row.visible && !row.hasScore() && !(row.graphGroup > -1
+ && graphGroupSeen.get(row.graphGroup)))
+ {
+ continue;
+ }
+
+ color = null;
+ oneColour = true;
+
+ // mark any sequence references for the row
+ writeSequence_Ref(refSeq, row.sequenceRef);
+ refSeq = row.sequenceRef;
+ // mark any group references for the row
+ writeGroup_Ref(refGroup, row.groupRef);
+ refGroup = row.groupRef;
+
+ boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText,
+ hasValues = row.hasScore, hasText = false;
+ // lookahead to check what the annotation row object actually contains.
+ for (int j = 0; row.annotations != null
+ && j < row.annotations.length
+ && (!hasGlyphs || !hasLabels || !hasValues); j++)
+ {
+ if (row.annotations[j] != null)
+ {
+ hasLabels |= (row.annotations[j].displayCharacter != null
+ && row.annotations[j].displayCharacter.length() > 0
+ && !row.annotations[j].displayCharacter.equals(" "));
+ hasGlyphs |= (row.annotations[j].secondaryStructure != 0
+ && row.annotations[j].secondaryStructure != ' ');
+ hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't
+ // be
+ // rendered..
+ hasText |= (row.annotations[j].description != null
+ && row.annotations[j].description.length() > 0);
+ }
+ }
+
+ if (row.graph == AlignmentAnnotation.NO_GRAPH)
+ {
+ text.append("NO_GRAPH\t");
+ hasValues = false; // only secondary structure
+ // hasLabels = false; // and annotation description string.
+ }
+ else
+ {
+ if (row.graph == AlignmentAnnotation.BAR_GRAPH)
+ {
+ text.append("BAR_GRAPH\t");
+ hasGlyphs = false; // no secondary structure
+
+ }
+ else if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+ {
+ hasGlyphs = false; // no secondary structure
+ text.append("LINE_GRAPH\t");
+ }
+
+ if (row.getThreshold() != null)
+ {
+ graphLine.append("GRAPHLINE\t");
+ graphLine.append(row.label);
+ graphLine.append("\t");
+ graphLine.append(row.getThreshold().value);
+ graphLine.append("\t");
+ graphLine.append(row.getThreshold().label);
+ graphLine.append("\t");
+ graphLine.append(jalview.util.Format
+ .getHexString(row.getThreshold().colour));
+ graphLine.append(newline);
+ }
+
+ if (row.graphGroup > -1)
+ {
+ graphGroupSeen.set(row.graphGroup);
+ Integer key = new Integer(row.graphGroup);
+ if (graphGroup.containsKey(key))
+ {
+ graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
+
+ }
+ else
+ {
+ graphGroup_refs.put(key, new Object[] { refSeq, refGroup });
+ graphGroup.put(key, row.label);
+ }
+ }
+ }
+
+ text.append(row.label + "\t");
+ if (row.description != null)
+ {
+ text.append(row.description + "\t");
+ }
+ for (int j = 0; row.annotations != null
+ && j < row.annotations.length; j++)
+ {
+ if (refSeq != null
+ && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
+ {
+ continue;
+ }
+
+ if (row.annotations[j] != null)
+ {
+ comma = "";
+ if (hasGlyphs) // could be also hasGlyphs || ...
+ {
+
+ text.append(comma);
+ if (row.annotations[j].secondaryStructure != ' ')
+ {
+ // only write out the field if its not whitespace.
+ text.append(row.annotations[j].secondaryStructure);
+ }
+ comma = ",";
+ }
+ if (hasValues)
+ {
+ if (!Float.isNaN(row.annotations[j].value))
+ {
+ text.append(comma + row.annotations[j].value);
+ }
+ else
+ {
+ // System.err.println("Skipping NaN - not valid value.");
+ text.append(comma + 0f);// row.annotations[j].value);
+ }
+ comma = ",";
+ }
+ if (hasLabels)
+ {
+ // TODO: labels are emitted after values for bar graphs.
+ if // empty labels are allowed, so
+ (row.annotations[j].displayCharacter != null
+ && row.annotations[j].displayCharacter.length() > 0
+ && !row.annotations[j].displayCharacter.equals(" "))
+ {
+ text.append(comma + row.annotations[j].displayCharacter);
+ comma = ",";
+ }
+ }
+ if (hasText)
+ {
+ if (row.annotations[j].description != null
+ && row.annotations[j].description.length() > 0
+ && !row.annotations[j].description
+ .equals(row.annotations[j].displayCharacter))
+ {
+ text.append(comma + row.annotations[j].description);
+ comma = ",";
+ }
+ }
+ if (color != null && !color.equals(row.annotations[j].colour))
+ {
+ oneColour = false;
+ }
+
+ color = row.annotations[j].colour;
+
+ if (row.annotations[j].colour != null
+ && row.annotations[j].colour != java.awt.Color.black)
+ {
+ text.append(comma + "[" + jalview.util.Format
+ .getHexString(row.annotations[j].colour) + "]");
+ comma = ",";
+ }
+ }
+ text.append("|");
+ }
+
+ if (row.hasScore())
+ {
+ text.append("\t" + row.score);
+ }
+
+ text.append(newline);
+
+ if (color != null && color != java.awt.Color.black && oneColour)
+ {
+ colours.append("COLOUR\t");
+ colours.append(row.label);
+ colours.append("\t");
+ colours.append(jalview.util.Format.getHexString(color));
+ colours.append(newline);
+ }
+ if (row.scaleColLabel || row.showAllColLabels
+ || row.centreColLabels)
+ {
+ rowprops.append("ROWPROPERTIES\t");
+ rowprops.append(row.label);
+ rowprops.append("\tscaletofit=");
+ rowprops.append(row.scaleColLabel);
+ rowprops.append("\tshowalllabs=");
+ rowprops.append(row.showAllColLabels);
+ rowprops.append("\tcentrelabs=");
+ rowprops.append(row.centreColLabels);
+ rowprops.append(newline);
+ }
+ if (graphLine.length() > 0)
+ {
+ text.append(graphLine.toString());
+ graphLine.setLength(0);
+ }
+ }
+
+ text.append(newline);
+
+ text.append(colours.toString());
+ if (graphGroup.size() > 0)
+ {
+ SequenceI oldRefSeq = refSeq;
+ SequenceGroup oldRefGroup = refGroup;
+ for (Map.Entry combine_statement : graphGroup
+ .entrySet())
+ {
+ Object[] seqRefAndGroup = graphGroup_refs
+ .get(combine_statement.getKey());
+
+ writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]);
+ refSeq = (SequenceI) seqRefAndGroup[0];
+
+ writeGroup_Ref(refGroup, (SequenceGroup) seqRefAndGroup[1]);
+ refGroup = (SequenceGroup) seqRefAndGroup[1];
+ text.append("COMBINE\t");
+ text.append(combine_statement.getValue());
+ text.append(newline);
+ }
+ writeSequence_Ref(refSeq, oldRefSeq);
+ refSeq = oldRefSeq;
+
+ writeGroup_Ref(refGroup, oldRefGroup);
+ refGroup = oldRefGroup;
+ }
+ text.append(rowprops.toString());
+ }
+
+ if (list != null)
+ {
+ printGroups(list);
+ }
+
+ if (properties != null)
+ {
+ text.append(newline);
+ text.append(newline);
+ text.append("ALIGNMENT");
+ Enumeration en = properties.keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ text.append("\t");
+ text.append(key);
+ text.append("=");
+ text.append(properties.get(key));
+ }
+ // TODO: output alignment visualization settings here if required
+ // iterate through one or more views, defining, marking columns and rows
+ // as visible/hidden, and emmitting view properties.
+ // View specific annotation is
+ }
+
+ return text.toString();
+ }
+
+ private Object writeGroup_Ref(SequenceGroup refGroup,
+ SequenceGroup next_refGroup)
+ {
+ if (next_refGroup == null)
+ {
+
+ if (refGroup != null)
+ {
+ text.append(newline);
+ text.append("GROUP_REF\t");
+ text.append("ALIGNMENT");
+ text.append(newline);
+ }
+ return true;
+ }
+ else
+ {
+ if (refGroup == null || refGroup != next_refGroup)
+ {
+ text.append(newline);
+ text.append("GROUP_REF\t");
+ text.append(next_refGroup.getName());
+ text.append(newline);
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
+ {
+
+ if (next_refSeq == null)
+ {
+ if (refSeq != null)
+ {
+ text.append(newline);
+ text.append("SEQUENCE_REF\t");
+ text.append("ALIGNMENT");
+ text.append(newline);
+ return true;
+ }
+ }
+ else
+ {
+ if (refSeq == null || refSeq != next_refSeq)
+ {
+ text.append(newline);
+ text.append("SEQUENCE_REF\t");
+ text.append(next_refSeq.getName());
+ text.append(newline);
+ return true;
+ }
+ }
+ return false;
+ }
+
+ protected void printGroups(List list)
+ {
+ SequenceI seqrep = null;
+ for (SequenceGroup sg : list)
+ {
+ if (!sg.hasSeqrep())
+ {
+ text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
+ + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)
+ + "\t" + "-1\t");
+ seqrep = null;
+ }
+ else
+ {
+ seqrep = sg.getSeqrep();
+ text.append("SEQUENCE_REF\t");
+ text.append(seqrep.getName());
+ text.append(newline);
+ text.append("SEQUENCE_GROUP\t");
+ text.append(sg.getName());
+ text.append("\t");
+ text.append((seqrep.findPosition(sg.getStartRes())));
+ text.append("\t");
+ text.append((seqrep.findPosition(sg.getEndRes())));
+ text.append("\t");
+ text.append("-1\t");
+ }
+ for (int s = 0; s < sg.getSize(); s++)
+ {
+ text.append(sg.getSequenceAt(s).getName());
+ text.append("\t");
+ }
+ text.append(newline);
+ text.append("PROPERTIES\t");
+ text.append(sg.getName());
+ text.append("\t");
+
+ if (sg.getDescription() != null)
+ {
+ text.append("description=");
+ text.append(sg.getDescription());
+ text.append("\t");
+ }
+ if (sg.cs != null)
+ {
+ text.append("colour=");
+ text.append(ColourSchemeProperty
+ .getColourName(sg.cs.getColourScheme()));
+ text.append("\t");
+ if (sg.cs.getThreshold() != 0)
+ {
+ text.append("pidThreshold=");
+ text.append(sg.cs.getThreshold());
+ }
+ if (sg.cs.conservationApplied())
+ {
+ text.append("consThreshold=");
+ text.append(sg.cs.getConservationInc());
+ text.append("\t");
+ }
+ }
+ text.append("outlineColour=");
+ text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
+ text.append("\t");
+
+ text.append("displayBoxes=");
+ text.append(sg.getDisplayBoxes());
+ text.append("\t");
+ text.append("displayText=");
+ text.append(sg.getDisplayText());
+ text.append("\t");
+ text.append("colourText=");
+ text.append(sg.getColourText());
+ text.append("\t");
+ text.append("showUnconserved=");
+ text.append(sg.getShowNonconserved());
+ text.append("\t");
+ if (sg.textColour != java.awt.Color.black)
+ {
+ text.append("textCol1=");
+ text.append(jalview.util.Format.getHexString(sg.textColour));
+ text.append("\t");
+ }
+ if (sg.textColour2 != java.awt.Color.white)
+ {
+ text.append("textCol2=");
+ text.append(jalview.util.Format.getHexString(sg.textColour2));
+ text.append("\t");
+ }
+ if (sg.thresholdTextColour != 0)
+ {
+ text.append("textColThreshold=");
+ text.append(sg.thresholdTextColour);
+ text.append("\t");
+ }
+ if (sg.idColour != null)
+ {
+ text.append("idColour=");
+ text.append(jalview.util.Format.getHexString(sg.idColour));
+ text.append("\t");
+ }
+ if (sg.isHidereps())
+ {
+ text.append("hide=true\t");
+ }
+ if (sg.isHideCols())
+ {
+ text.append("hidecols=true\t");
+ }
+ if (seqrep != null)
+ {
+ // terminate the last line and clear the sequence ref for the group
+ text.append(newline);
+ text.append("SEQUENCE_REF");
+ }
+ text.append(newline);
+ text.append(newline);
+
+ }
+ }
+
+ SequenceI refSeq = null;
+
+ String refSeqId = null;
+
+ public boolean annotateAlignmentView(AlignViewportI viewport, Object file,
+ DataSourceType protocol)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+ HiddenColumns hidden = viewport.getAlignment().getHiddenColumns();
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ if (hidden == null)
+ {
+ hidden = new HiddenColumns();
+ }
+ boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden, file,
+ protocol);
+ if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns()))
+ {
+ viewport.setColumnSelection(colSel);
+ viewport.getAlignment().setHiddenColumns(hidden);
+ }
+
+ return rslt;
+ }
+
+ public boolean readAnnotationFile(AlignmentI al, String file,
+ DataSourceType sourceType)
+ {
+ return readAnnotationFile(al, null, file, sourceType);
+ }
+
+ public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
+ Object file, DataSourceType sourceType)
+ {
+ BufferedReader in = null;
+ try
+ {
+ if (sourceType == DataSourceType.FILE)
+ {
+ in = FileLoader.getBuffereReader(file);
+ }
+ else if (sourceType == DataSourceType.URL)
+ {
+ URL url = new URL(file.toString());
+ in = new BufferedReader(new InputStreamReader(url.openStream()));
+ }
+ else if (sourceType == DataSourceType.PASTE)
+ {
+ in = new BufferedReader(new StringReader(file.toString()));
+ }
+ else if (sourceType == DataSourceType.CLASSLOADER)
+ {
+ java.io.InputStream is = getClass().getResourceAsStream("/" + file);
+ if (is != null)
+ {
+ in = new BufferedReader(new java.io.InputStreamReader(is));
+ }
+ }
+ if (in != null)
+ {
+ return parseAnnotationFrom(al, hidden, in);
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ System.out.println("Problem reading annotation file: " + ex);
+ if (nlinesread > 0)
+ {
+ System.out.println("Last read line " + nlinesread + ": '" + lastread
+ + "' (first 80 chars) ...");
+ }
+ return false;
+ }
+ return false;
+ }
+
+ long nlinesread = 0;
+
+ String lastread = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
+
+ public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,
+ BufferedReader in) throws Exception
+ {
+ nlinesread = 0;
+ ArrayList