X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=ae34f6b8c1b42e7d9b3b4a5fbe12bbd5ae262ec4;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=581d9cc1bb79aebc5ea66e35ce18d6fd8d1de1d5;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 581d9cc..ae34f6b 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,1382 +1,1799 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * 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 .
- */
-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");
-
- /**
- * convenience method for pre-2.4 feature files which have no view, hidden
- * columns or hidden row keywords.
- *
- * @param annotations
- * @param groups
- * @param properties
- * @return feature file as a string.
- */
- public String printAnnotations(AlignmentAnnotation[] annotations,
- Vector groups, Hashtable properties)
- {
- return printAnnotations(annotations, groups, properties, null);
-
- }
-
- /**
- * hold all the information about a particular view definition read from or
- * written out in an annotations file.
- */
- public class ViewDef
- {
- public String viewname;
-
- public HiddenSequences hidseqs;
-
- public ColumnSelection hiddencols;
-
- public Vector visibleGroups;
-
- public Hashtable hiddenRepSeqs;
-
- public ViewDef(String viewname, HiddenSequences hidseqs,
- ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
- {
- this.viewname = viewname;
- this.hidseqs = hidseqs;
- this.hiddencols = hiddencols;
- this.hiddenRepSeqs = hiddenRepSeqs;
- }
- }
-
- /**
- * Prepare an annotation file given a set of annotations, groups, alignment
- * properties and views.
- *
- * @param annotations
- * @param groups
- * @param properties
- * @param views
- * @return annotation file
- */
- public String printAnnotations(AlignmentAnnotation[] annotations,
- Vector groups, Hashtable properties, ViewDef[] views)
- {
- // TODO: resolve views issue : annotationFile could contain visible region,
- // or full data + hidden region specifications for a view.
- 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();
-
- java.awt.Color color;
-
- for (int i = 0; i < annotations.length; i++)
- {
- row = annotations[i];
-
- if (!row.visible && !row.hasScore())
- {
- continue;
- }
-
- color = null;
- oneColour = true;
-
- 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");
- }
- }
- // mark any group references for the row
- if (row.groupRef == null)
- {
-
- if (refGroup != null)
- {
- text.append("\nGROUP_REF\tALIGNMENT\n");
- }
-
- refGroup = null;
- }
- else
- {
- if (refGroup == null || refGroup != row.groupRef)
- {
- refGroup = row.groupRef;
- text.append("\nGROUP_REF\t" + refGroup.getName() + "\n");
- }
- }
-
- 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 |= (row.annotations[j].value != Float.NaN); // 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"
- + 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; 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 (row.annotations[j].value != Float.NaN)
- {
- 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("\n");
-
- if (color != null && color != java.awt.Color.black && oneColour)
- {
- colours.append("COLOUR\t" + row.label + "\t"
- + jalview.util.Format.getHexString(color) + "\n");
- }
- if (row.scaleColLabel || row.showAllColLabels
- || row.centreColLabels)
- {
- rowprops.append("ROWPROPERTIES\t" + row.label);
- rowprops.append("\tscaletofit=" + row.scaleColLabel);
- rowprops.append("\tshowalllabs=" + row.showAllColLabels);
- rowprops.append("\tcentrelabs=" + row.centreColLabels);
- rowprops.append("\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");
- }
- }
- text.append(rowprops.toString());
- }
-
- 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));
- }
- // TODO: output alignment visualization settings here if required
-
- }
-
- return text.toString();
- }
-
- public void printGroups(Vector sequenceGroups)
- {
- SequenceGroup sg;
- SequenceI seqrep = null;
- for (int i = 0; i < sequenceGroups.size(); i++)
- {
- sg = (SequenceGroup) sequenceGroups.elementAt(i);
- 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" + seqrep.getName() + "\n");
- text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
- + (seqrep.findPosition(sg.getStartRes())) + "\t"
- + (seqrep.findPosition(sg.getEndRes())) + "\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");
- text.append("showUnconserved=" + sg.getShowNonconserved() + "\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 + "\t");
- }
- if (sg.idColour != null)
- {
- text.append("idColour="
- + jalview.util.Format.getHexString(sg.idColour) + "\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("\nSEQUENCE_REF");
- }
- text.append("\n\n");
-
- }
- }
-
- SequenceI refSeq = null;
-
- String refSeqId = null;
-
- public boolean readAnnotationFile(AlignmentI al, String file,
- String protocol)
- {
- String groupRef = null;
- Hashtable groupRefRows = new Hashtable();
-
- Hashtable autoAnnots = new Hashtable();
- 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;
- // when true - will add new rows regardless of whether they are duplicate
- // auto-annotation like consensus or conservation graphs
- boolean overrideAutoAnnot = false;
- if (al.getAlignmentAnnotation() != null)
- {
- existingAnnotations = al.getAlignmentAnnotation().length;
- if (existingAnnotations > 0)
- {
- AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
- for (int aai = 0; aai < aa.length; aai++)
- {
- if (aa[aai].autoCalculated)
- {
- // make a note of the name and description
- autoAnnots.put(aa[aai].graph
- + "\t"
- + aa[aai].label
- + "\t"
- + aa[aai].description
- + "\t"
- + (aa[aai].sequenceRef != null ? aa[aai].sequenceRef
- .getDisplayId(true) : ""), new Integer(1));
- }
- }
- }
- }
-
- 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"))
- {
- // TODO: use graduated colour def'n here too
- colourAnnotations(al, st.nextToken(), st.nextToken());
- continue;
- }
-
- else if (token.equalsIgnoreCase("COMBINE"))
- {
- combineAnnotations(al, st);
- continue;
- }
- else if (token.equalsIgnoreCase("ROWPROPERTIES"))
- {
- addRowProperties(al, st);
- continue;
- }
- else if (token.equalsIgnoreCase("GRAPHLINE"))
- {
- addLine(al, st);
- continue;
- }
-
- else if (token.equalsIgnoreCase("SEQUENCE_REF"))
- {
- if (st.hasMoreTokens())
- {
- refSeq = al.findName(refSeqId = st.nextToken());
- if (refSeq == null)
- {
- refSeqId = null;
- }
- 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;
- }
- }
- else
- {
- refSeq = null;
- refSeqId = null;
- }
- continue;
- }
- else if (token.equalsIgnoreCase("GROUP_REF"))
- {
- // Group references could be forward or backwards, so they are
- // resolved after the whole file is read in
- groupRef = null;
- if (st.hasMoreTokens())
- {
- groupRef = st.nextToken();
- if (groupRef.length() < 1)
- {
- groupRef = null; // empty string
- }
- else
- {
- if (groupRefRows.get(groupRef) == null)
- {
- groupRefRows.put(groupRef, new Vector());
- }
- }
- }
- 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;
- }
-
- // Parse out the annotation row
- 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, graphStyle);
- emptyColumn = false;
- }
- }
-
- }
-
- annotation = new AlignmentAnnotation(label, description,
- (index == 0) ? null : annotations, 0, 0, graphStyle);
-
- annotation.score = score;
- if (!overrideAutoAnnot
- && autoAnnots
- .containsKey(annotation.graph
- + "\t"
- + annotation.label
- + "\t"
- + annotation.description
- + "\t"
- + (refSeq != null ? refSeq
- .getDisplayId(true) : "")))
- {
- // skip - we've already got an automatic annotation of this type.
- continue;
- }
- // otherwise add it!
- if (refSeq != null)
- {
-
- annotation.belowAlignment = false;
- // make a copy of refSeq so we can find other matches in the alignment
- SequenceI referedSeq = refSeq;
- do
- {
- // copy before we do any mapping business.
- // TODO: verify that undo/redo with 1:many sequence associated
- // annotations can be undone correctly
- AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
- annotation
- .createSequenceMapping(referedSeq, refSeqIndex, false);
- annotation.adjustForAlignment();
- referedSeq.addAlignmentAnnotation(annotation);
- al.addAnnotation(annotation);
- al.setAnnotationIndex(annotation,
- al.getAlignmentAnnotation().length
- - existingAnnotations - 1);
- if (groupRef != null)
- {
- ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
- }
- // and recover our virgin copy to use again if necessary.
- annotation = ann;
-
- } while (refSeqId != null
- && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
- }
- else
- {
- al.addAnnotation(annotation);
- al.setAnnotationIndex(annotation,
- al.getAlignmentAnnotation().length - existingAnnotations
- - 1);
- if (groupRef != null)
- {
- ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
- }
- }
- }
- // Finally, resolve the groupRefs
- Enumeration en = groupRefRows.keys();
- SequenceGroup theGroup = null;
-
- while (en.hasMoreElements())
- {
- groupRef = (String) en.nextElement();
- boolean matched = false;
- // Resolve group: TODO: add a getGroupByName method to alignments
- Vector grps = al.getGroups();
- for (int g = 0, gSize = grps.size(); g < gSize; g++)
- {
- theGroup = (SequenceGroup) grps.elementAt(g);
- if (theGroup.getName().equals(groupRef))
- {
- if (matched)
- {
- // TODO: specify and implement duplication of alignment annotation
- // for multiple group references.
- System.err
- .println("Ignoring 1:many group reference mappings for group name '"
- + groupRef + "'");
- }
- else
- {
- matched = true;
- Vector rowset = (Vector) groupRefRows.get(groupRef);
- if (rowset != null && rowset.size() > 0)
- {
- AlignmentAnnotation alan = null;
- for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
- {
- alan = (AlignmentAnnotation) rowset.elementAt(elm);
- alan.groupRef = theGroup;
- }
- }
- }
- }
- }
- ((Vector) groupRefRows.get(groupRef)).removeAllElements();
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- System.out.println("Problem reading annotation file: " + ex);
- return false;
- }
- return true;
- }
-
- Annotation parseAnnotation(String string, int graphStyle)
- {
- boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
- // do the
- // glyph
- // test
- // if we
- // don't
- // want
- // secondary
- // structure
- String desc = null, displayChar = null;
- char ss = ' '; // secondaryStructure
- float value = 0;
- boolean parsedValue = false, dcset = 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));
- if (i > 0 && string.charAt(i - 1) == ',')
- {
- // clip the preceding comma as well
- i--;
- }
- string = string.substring(0, i) + string.substring(j + 1);
- }
-
- StringTokenizer st = new StringTokenizer(string, ",", true);
- String token;
- boolean seenContent = false;
- int pass = 0;
- while (st.hasMoreTokens())
- {
- pass++;
- token = st.nextToken().trim();
- if (token.equals(","))
- {
- if (!seenContent && parsedValue && !dcset)
- {
- // allow the value below the bar/line to be empty
- dcset = true;
- displayChar = " ";
- }
- seenContent = false;
- continue;
- }
- else
- {
- seenContent = true;
- }
-
- if (!parsedValue)
- {
- try
- {
- displayChar = token;
- // foo
- value = new Float(token).floatValue();
- parsedValue = true;
- continue;
- } catch (NumberFormatException ex)
- {
- }
- }
- else
- {
- if (token.length() == 1)
- {
- displayChar = token;
- }
- }
- if (hasSymbols
- && (token.equals("H") || token.equals("E") || token
- .equals(" ")))
- {
- // 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 || (parsedValue && pass > 2))
- {
- desc = token;
- }
-
- }
- // if (!dcset && string.charAt(string.length() - 1) == ',')
- // {
- // displayChar = " "; // empty display char symbol.
- // }
- if (displayChar != null && desc != null && desc.length() == 1)
- {
- if (displayChar.length() > 1)
- {
- // switch desc and displayChar - legacy support
- String tmp = displayChar;
- displayChar = desc;
- desc = tmp;
- }
- else
- {
- if (displayChar.equals(desc))
- {
- // duplicate label - hangover from the 'robust parser' above
- desc = null;
- }
- }
- }
- 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
- if (al.getAlignmentAnnotation() != null)
- {
- 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;
- }
- }
- }
- }
- else
- {
- System.err
- .println("Couldn't combine annotations. None are added to alignment yet!");
- }
- }
-
- void addLine(AlignmentI al, StringTokenizer st)
- {
- String group = st.nextToken();
- AlignmentAnnotation annotation = null, alannot[] = al
- .getAlignmentAnnotation();
- if (alannot != null)
- {
- for (int i = 0; i < alannot.length; i++)
- {
- if (alannot[i].label.equalsIgnoreCase(group))
- {
- annotation = alannot[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());
- String rng = "";
- try
- {
- rng = st.nextToken();
- if (rng.length() > 0 && !rng.startsWith("*"))
- {
- sg.setStartRes(Integer.parseInt(rng) - 1);
- }
- else
- {
- sg.setStartRes(0);
- }
- rng = st.nextToken();
- if (rng.length() > 0 && !rng.startsWith("*"))
- {
- sg.setEndRes(Integer.parseInt(rng) - 1);
- }
- else
- {
- sg.setEndRes(al.getWidth() - 1);
- }
- } catch (Exception e)
- {
- System.err
- .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
- + rng + "' - assuming alignment width for group.");
- // assume group is full width
- sg.setStartRes(0);
- sg.setEndRes(al.getWidth() - 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);
- sg.setSeqrep(refSeq);
- }
-
- if (sg.getSize() > 0)
- {
- al.addGroup(sg);
- }
- }
-
- void addRowProperties(AlignmentI al, StringTokenizer st)
- {
- String label = st.nextToken(), keyValue, key, value;
- boolean scaletofit = false, centerlab = false, showalllabs = false;
- while (st.hasMoreTokens())
- {
- keyValue = st.nextToken();
- key = keyValue.substring(0, keyValue.indexOf("="));
- value = keyValue.substring(keyValue.indexOf("=") + 1);
- if (key.equalsIgnoreCase("scaletofit"))
- {
- scaletofit = Boolean.valueOf(value).booleanValue();
- }
- if (key.equalsIgnoreCase("showalllabs"))
- {
- showalllabs = Boolean.valueOf(value).booleanValue();
- }
- if (key.equalsIgnoreCase("centrelabs"))
- {
- centerlab = Boolean.valueOf(value).booleanValue();
- }
- AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
- if (alr != null)
- {
- for (int i = 0; i < alr.length; i++)
- {
- if (alr[i].label.equalsIgnoreCase(label))
- {
- alr[i].centreColLabels = centerlab;
- alr[i].scaleColLabel = scaletofit;
- alr[i].showAllColLabels = showalllabs;
- }
- }
- }
- }
- }
-
- 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;
- ColourSchemeI def = sg.cs;
- sg.cs = null;
- 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("showUnconserved"))
- {
- sg.setShowNonconserved(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);
- }
- else if (key.equalsIgnoreCase("idColour"))
- {
- // consider warning if colour doesn't resolve to a real colour
- sg.setIdColour((def = new UserColourScheme(value))
- .findColour('A'));
- }
- else if (key.equalsIgnoreCase("hide"))
- {
- // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
- sg.setHidereps(true);
- }
- else if (key.equalsIgnoreCase("hidecols"))
- {
- // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847
- sg.setHideCols(true);
- }
- sg.recalcConservation();
- }
- if (sg.cs == null)
- {
- sg.cs = def;
- }
- }
- }
-
- void setBelowAlignment(AlignmentI al, StringTokenizer st)
- {
- String token;
- AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
- if (ala == null)
- {
- System.err
- .print("Warning - no annotation to set below for sequence associated annotation:");
- }
- while (st.hasMoreTokens())
- {
- token = st.nextToken();
- if (ala == null)
- {
- System.err.print(" "+token);
- }
- else
- {
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
- {
- aa = al.getAlignmentAnnotation()[i];
- if (aa.sequenceRef == refSeq && aa.label.equals(token))
- {
- aa.belowAlignment = true;
- }
- }
- }
- }
- if (ala==null)
- {
- System.err.print("\n");
- }
- }
-
- void addAlignmentDetails(AlignmentI al, StringTokenizer st)
- {
- String keyValue, key, value;
- while (st.hasMoreTokens())
- {
- keyValue = st.nextToken();
- key = keyValue.substring(0, keyValue.indexOf("="));
- value = keyValue.substring(keyValue.indexOf("=") + 1);
- al.setProperty(key, value);
- }
- }
-
- /**
- * Write annotations as a CSV file of the form 'label, value, value, ...' for
- * each row.
- *
- * @param annotations
- * @return CSV file as a string.
- */
- public String printCSVAnnotations(AlignmentAnnotation[] annotations)
- {
- StringBuffer sp = new StringBuffer();
- for (int i = 0; i < annotations.length; i++)
- {
- String atos = annotations[i].toString();
- int p = 0;
- do
- {
- int cp = atos.indexOf("\n", p);
- sp.append(annotations[i].label);
- sp.append(",");
- if (cp > p)
- {
- sp.append(atos.substring(p, cp + 1));
- }
- else
- {
- sp.append(atos.substring(p));
- sp.append("\n");
- }
- p = cp + 1;
- } while (p > 0);
- }
- return sp.toString();
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * 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.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
+ {
+ public String viewname;
+
+ public HiddenSequences hidseqs;
+
+ public ColumnSelection hiddencols;
+
+ public Vector visibleGroups;
+
+ public Hashtable hiddenRepSeqs;
+
+ public ViewDef(String viewname, HiddenSequences hidseqs,
+ ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+ {
+ this.viewname = viewname;
+ this.hidseqs = hidseqs;
+ this.hiddencols = hiddencols;
+ this.hiddenRepSeqs = hiddenRepSeqs;
+ }
+ }
+
+ /**
+ * 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,
+ ColumnSelection 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");
+ List hc = cs.getHiddenColumns();
+ boolean comma = false;
+ for (int[] r : hc)
+ {
+ if (!comma)
+ {
+ comma = true;
+ }
+ else
+ {
+ text.append(",");
+ }
+ text.append(r[0]);
+ text.append("-");
+ text.append(r[1]);
+ }
+ 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;
+ }
+
+ public 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(sg.cs.toString());
+ 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,
+ String file, DataSourceType protocol)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
+ file, protocol);
+ if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+ {
+ viewport.setColumnSelection(colSel);
+ }
+
+ return rslt;
+ }
+
+ public boolean readAnnotationFile(AlignmentI al, String file,
+ DataSourceType sourceType)
+ {
+ return readAnnotationFile(al, null, file, sourceType);
+ }
+
+ public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
+ String file, DataSourceType sourceType)
+ {
+ BufferedReader in = null;
+ try
+ {
+ if (sourceType == DataSourceType.FILE)
+ {
+ in = new BufferedReader(new FileReader(file));
+ }
+ else if (sourceType == DataSourceType.URL)
+ {
+ URL url = new URL(file);
+ in = new BufferedReader(new InputStreamReader(url.openStream()));
+ }
+ else if (sourceType == DataSourceType.PASTE)
+ {
+ in = new BufferedReader(new StringReader(file));
+ }
+ 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, colSel, 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, ColumnSelection colSel,
+ BufferedReader in) throws Exception
+ {
+ nlinesread = 0;
+ ArrayList