X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=44c7f2e5efb53845de2b60d2c17bf48249c4c8bf;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=a936dac86b2fc4245f3c10a297a406600a4c4ed4;hpb=b5fdf35e68eea0a0710cae2178020645ac17e6af;p=jalview.git
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index a936dac..44c7f2e 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,22 +1,20 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.*;
@@ -29,24 +27,110 @@ import jalview.schemes.*;
public class AnnotationFile
{
- StringBuffer text = new StringBuffer(
- "JALVIEW_ANNOTATION\n"
- + "# Created: "
- + new java.util.Date() + "\n\n");
+ 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-2.4 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)
+ 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;
@@ -55,53 +139,114 @@ public class AnnotationFile
{
row = annotations[i];
- if (!row.visible)
+ if (!row.visible && !row.hasScore())
{
continue;
}
color = null;
+ oneColour = true;
if (row.sequenceRef == null)
{
if (refSeq != null)
{
- text.append("\nSEQUENCE_REF\tALIGNMENT\n");
+ text.append(newline);
+ text.append("SEQUENCE_REF\tALIGNMENT");
+ text.append(newline);
}
refSeq = null;
}
- else if (refSeq == null || refSeq != row.sequenceRef)
+ else
{
- refSeq = row.sequenceRef;
- text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
+ if (refSeq == null || refSeq != row.sequenceRef)
+ {
+ refSeq = row.sequenceRef;
+ text.append(newline);
+ text.append("SEQUENCE_REF\t");
+ text.append(refSeq.getName());
+ text.append(newline);
+ }
+ }
+ // mark any group references for the row
+ if (row.groupRef == null)
+ {
+
+ if (refGroup != null)
+ {
+ text.append(newline);
+ text.append("GROUP_REF\tALIGNMENT");
+ text.append(newline);
+ }
+
+ refGroup = null;
+ }
+ else
+ {
+ if (refGroup == null || refGroup != row.groupRef)
+ {
+ refGroup = row.groupRef;
+ text.append(newline);
+ text.append("GROUP_REF\t");
+ text.append(refGroup.getName());
+ text.append(newline);
+ }
+ }
+
+ 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"
- );
+ 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)
@@ -109,8 +254,7 @@ public class AnnotationFile
String key = String.valueOf(row.graphGroup);
if (graphGroup.containsKey(key))
{
- graphGroup.put(key, graphGroup.get(key)
- + "\t" + row.label);
+ graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
}
else
{
@@ -124,11 +268,11 @@ public class AnnotationFile
{
text.append(row.description + "\t");
}
-
- for (int j = 0; j < row.annotations.length; j++)
+ for (int j = 0; row.annotations != null
+ && j < row.annotations.length; j++)
{
- if (refSeq != null &&
- jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
+ if (refSeq != null
+ && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
{
continue;
}
@@ -136,54 +280,103 @@ public class AnnotationFile
if (row.annotations[j] != null)
{
comma = "";
- if (row.annotations[j].secondaryStructure != ' ')
+ if (hasGlyphs) // could be also hasGlyphs || ...
{
- text.append(comma + row.annotations[j].secondaryStructure);
+
+ 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 (row.annotations[j].displayCharacter!=null
- && row.annotations[j].displayCharacter.length() > 0
- && !row.annotations[j].displayCharacter.equals(" "))
+ if (hasValues)
{
- text.append(comma + row.annotations[j].displayCharacter);
+ 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 (row.annotations[j] != null)
+ if (hasLabels)
{
- color = row.annotations[j].colour;
- if (row.annotations[j].value != 0f)
+ // 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].value);
+ 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;
+ }
- if(row.annotations[j].colour!=null
- && row.annotations[j].colour!=java.awt.Color.black)
+ 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)+"]");
+ text.append(comma
+ + "["
+ + jalview.util.Format
+ .getHexString(row.annotations[j].colour)
+ + "]");
+ comma = ",";
}
}
text.append("|");
}
- if(!Float.isNaN(row.score))
- text.append("\t"+row.score);
+ if (row.hasScore())
+ text.append("\t" + row.score);
- text.append("\n");
+ text.append(newline);
- if (color != null && color != java.awt.Color.black)
+ if (color != null && color != java.awt.Color.black && oneColour)
{
- colours.append("COLOUR\t"
- + row.label + "\t"
- + jalview.util.Format.getHexString(color) + "\n");
+ 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);
}
-
}
- text.append("\n");
+ text.append(newline);
text.append(colours.toString());
text.append(graphLine.toString());
@@ -193,9 +386,11 @@ public class AnnotationFile
Enumeration en = graphGroup.elements();
while (en.hasMoreElements())
{
- text.append(en.nextElement() + "\n");
+ text.append(en.nextElement());
+ text.append(newline);
}
}
+ text.append(rowprops.toString());
}
if (groups != null)
@@ -203,15 +398,21 @@ public class AnnotationFile
printGroups(groups);
}
- if(properties!=null)
+ if (properties != null)
{
- text.append("\n\nALIGNMENT");
+ text.append(newline);
+ text.append(newline);
+ text.append("ALIGNMENT");
Enumeration en = properties.keys();
- while(en.hasMoreElements())
+ while (en.hasMoreElements())
{
String key = en.nextElement().toString();
- text.append("\t"+key+"="+properties.get(key));
+ text.append("\t");
+ text.append(key);
+ text.append("=");
+ text.append(properties.get(key));
}
+ // TODO: output alignment visualization settings here if required
}
@@ -221,73 +422,135 @@ public class AnnotationFile
public void printGroups(Vector sequenceGroups)
{
SequenceGroup sg;
+ SequenceI seqrep = null;
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");
+ 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() + "\t");
+ text.append(sg.getSequenceAt(s).getName());
+ text.append("\t");
}
-
- text.append("\nPROPERTIES\t" + sg.getName() + "\t");
+ text.append(newline);
+ text.append("PROPERTIES\t");
+ text.append(sg.getName());
+ text.append("\t");
if (sg.getDescription() != null)
{
- text.append("description=" + sg.getDescription() + "\t");
+ text.append("description=");
+ text.append(sg.getDescription());
+ text.append("\t");
}
if (sg.cs != null)
{
- text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs) +
- "\t");
+ text.append("colour=");
+ text.append(ColourSchemeProperty.getColourName(sg.cs));
+ text.append("\t");
if (sg.cs.getThreshold() != 0)
{
- text.append("pidThreshold=" + sg.cs.getThreshold());
+ text.append("pidThreshold=");
+ text.append(sg.cs.getThreshold());
}
if (sg.cs.conservationApplied())
{
- text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");
+ text.append("consThreshold=");
+ text.append(sg.cs.getConservationInc());
+ text.append("\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("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=" +
- jalview.util.Format.getHexString(sg.textColour) + "\t");
+ text.append("textCol1=");
+ text.append(jalview.util.Format.getHexString(sg.textColour));
+ text.append("\t");
}
if (sg.textColour2 != java.awt.Color.white)
{
- text.append("textCol2=" +
- jalview.util.Format.getHexString(sg.textColour2) + "\t");
+ text.append("textCol2=");
+ text.append(jalview.util.Format.getHexString(sg.textColour2));
+ text.append("\t");
}
if (sg.thresholdTextColour != 0)
{
- text.append("textColThreshold=" + sg.thresholdTextColour);
+ text.append("textColThreshold=");
+ text.append(sg.thresholdTextColour);
+ text.append("\t");
}
-
- text.append("\n\n");
+ 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;
- public boolean readAnnotationFile(AlignmentI al,
- String file,
- String protocol)
+
+ String refSeqId = null;
+
+ public boolean readAnnotationFile(AlignmentI al, String file,
+ String protocol)
{
+ BufferedReader in = null;
try
{
- BufferedReader in = null;
if (protocol.equals(AppletFormatAdapter.FILE))
{
in = new BufferedReader(new FileReader(file));
@@ -309,14 +572,55 @@ public class AnnotationFile
in = new BufferedReader(new java.io.InputStreamReader(is));
}
}
+ if (in != null)
+ {
+ return parseAnnotationFrom(al, in);
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ System.out.println("Problem reading annotation file: " + ex);
+ return false;
+ }
+ return false;
+ }
+
+ public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
+ throws Exception
+ {
+ boolean modified = false;
+ String groupRef = null;
+ Hashtable groupRefRows = new Hashtable();
+ Hashtable autoAnnots = new Hashtable();
+ {
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(
+ autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
+ (aa[aai].groupRef == null ? null
+ : aa[aai].groupRef.getName())),
+ new Integer(1));
+ }
+ }
+ }
}
int alWidth = al.getWidth();
@@ -327,7 +631,7 @@ public class AnnotationFile
// First confirm this is an Annotation file
boolean jvAnnotationFile = false;
- while ( (line = in.readLine()) != null)
+ while ((line = in.readLine()) != null)
{
if (line.indexOf("#") == 0)
{
@@ -347,11 +651,11 @@ public class AnnotationFile
return false;
}
- while ( (line = in.readLine()) != null)
+ while ((line = in.readLine()) != null)
{
if (line.indexOf("#") == 0
- || line.indexOf("JALVIEW_ANNOTATION") > -1
- || line.length() == 0)
+ || line.indexOf("JALVIEW_ANNOTATION") > -1
+ || line.length() == 0)
{
continue;
}
@@ -360,43 +664,83 @@ public class AnnotationFile
token = st.nextToken();
if (token.equalsIgnoreCase("COLOUR"))
{
+ // TODO: use graduated colour def'n here too
colourAnnotations(al, st.nextToken(), st.nextToken());
+ modified = true;
continue;
}
else if (token.equalsIgnoreCase("COMBINE"))
{
combineAnnotations(al, st);
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase("ROWPROPERTIES"))
+ {
+ addRowProperties(al, st);
+ modified = true;
continue;
}
-
else if (token.equalsIgnoreCase("GRAPHLINE"))
{
addLine(al, st);
+ modified = true;
continue;
}
else if (token.equalsIgnoreCase("SEQUENCE_REF"))
{
- refSeq = al.findName(st.nextToken());
- try
+ if (st.hasMoreTokens())
{
- refSeqIndex = Integer.parseInt(st.nextToken());
- if (refSeqIndex < 1)
+ 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;
- System.out.println(
- "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
}
}
- catch (Exception ex)
+ else
{
- refSeqIndex = 1;
+ refSeq = null;
+ refSeqId = null;
}
-
- continue ;
+ 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);
@@ -406,64 +750,67 @@ public class AnnotationFile
else if (token.equalsIgnoreCase("PROPERTIES"))
{
addProperties(al, st);
+ modified = true;
continue;
}
- else if( token.equalsIgnoreCase("BELOW_ALIGNMENT"))
+ else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
{
setBelowAlignment(al, st);
+ modified = true;
continue;
}
- else if( token.equalsIgnoreCase("ALIGNMENT"))
+ else if (token.equalsIgnoreCase("ALIGNMENT"))
{
addAlignmentDetails(al, st);
+ modified = true;
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())
+ if (st.hasMoreTokens())
{
line = st.nextToken();
- if (line.indexOf("|") ==-1)
+ if (line.indexOf("|") == -1)
{
description = line;
if (st.hasMoreTokens())
line = st.nextToken();
}
- if(st.hasMoreTokens())
+ if (st.hasMoreTokens())
{
- //This must be the score
+ // This must be the score
score = Float.valueOf(st.nextToken()).floatValue();
}
st = new StringTokenizer(line, "|", true);
-
boolean emptyColumn = true;
- boolean onlyOneElement = (st.countTokens()==1);
+ boolean onlyOneElement = (st.countTokens() == 1);
while (st.hasMoreElements() && index < alWidth)
{
token = st.nextToken().trim();
- if(onlyOneElement)
+ if (onlyOneElement)
{
try
{
score = Float.valueOf(token).floatValue();
break;
+ } catch (NumberFormatException ex)
+ {
}
- catch(NumberFormatException ex){}
}
if (token.equals("|"))
@@ -477,91 +824,202 @@ public class AnnotationFile
}
else
{
- annotations[index++] = parseAnnotation(token);
+ annotations[index++] = parseAnnotation(token, graphStyle);
emptyColumn = false;
}
}
}
- annotation = new AlignmentAnnotation(label,
- description,
- annotations,
- 0,
- 0,
- graphStyle);
+ annotation = new AlignmentAnnotation(label, description,
+ (index == 0) ? null : annotations, 0, 0, graphStyle);
annotation.score = score;
-
- if (refSeq != null)
+ if (!overrideAutoAnnot
+ && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
+ groupRef)))
{
- annotation.belowAlignment=false;
- annotation.createSequenceMapping(refSeq, refSeqIndex, false);
- annotation.adjustForAlignment();
- refSeq.addAlignmentAnnotation(annotation);
+ // skip - we've already got an automatic annotation of this type.
+ continue;
}
+ // otherwise add it!
+ if (refSeq != null)
+ {
- al.addAnnotation(annotation);
+ 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;
- al.setAnnotationIndex(annotation,
- al.getAlignmentAnnotation().length - existingAnnotations -
- 1);
+ } 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);
+ }
+ }
+ // and set modification flag
+ modified = true;
}
+ // 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;
+ return modified;
}
- Annotation parseAnnotation(String string)
+ private Object autoAnnotsKey(AlignmentAnnotation annotation,
+ SequenceI refSeq, String groupRef)
{
+ return annotation.graph + "\t" + annotation.label + "\t"
+ + annotation.description + "\t"
+ + (refSeq != null ? refSeq.getDisplayId(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;
+ boolean parsedValue = false, dcset = false;
- //find colour here
+ // find colour here
java.awt.Color colour = null;
- int i=string.indexOf("[");
- int j=string.indexOf("]");
- if(i>-1 && j>-1)
+ 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);
+ 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, ",");
+ StringTokenizer st = new StringTokenizer(string, ",", true);
String token;
+ boolean seenContent = false;
+ int pass = 0;
while (st.hasMoreTokens())
{
+ pass++;
token = st.nextToken().trim();
- if (token.length() == 0)
+ 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)
+ {
}
- catch (NumberFormatException ex)
- {}
}
-
- if (token.equals("H") || token.equals("E"))
+ else
+ {
+ if (token.length() == 1)
+ {
+ displayChar = token;
+ }
+ }
+ if (hasSymbols
+ && (token.equals("H") || token.equals("E") || token.equals("S") || token
+ .equals(" ")))
{
// Either this character represents a helix or sheet
// or an integer which can be displayed
@@ -571,22 +1029,34 @@ public class AnnotationFile
displayChar = "";
}
}
- else if (desc == null)
+ else if (desc == null || (parsedValue && pass > 2))
{
desc = token;
}
}
-
- if (displayChar.length() > 1
- && desc!=null
- && desc.length() == 1)
+ // if (!dcset && string.charAt(string.length() - 1) == ',')
+ // {
+ // displayChar = " "; // empty display char symbol.
+ // }
+ if (displayChar != null && desc != null && desc.length() == 1)
{
- String tmp = displayChar;
- displayChar = desc;
- desc = tmp;
+ 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;
@@ -618,46 +1088,56 @@ public class AnnotationFile
{
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())
+ // First make sure we are not overwriting the graphIndex
+ if (al.getAlignmentAnnotation() != null)
{
- group = st.nextToken();
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;
-
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
+ AlignmentAnnotation annotation = null, alannot[] = al
+ .getAlignmentAnnotation();
+ if (alannot != null)
{
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))
+ for (int i = 0; i < alannot.length; i++)
{
- annotation = al.getAlignmentAnnotation()[i];
- break;
+ if (alannot[i].label.equalsIgnoreCase(group))
+ {
+ annotation = alannot[i];
+ break;
+ }
}
}
-
if (annotation == null)
{
return;
@@ -678,8 +1158,36 @@ public class AnnotationFile
{
SequenceGroup sg = new SequenceGroup();
sg.setName(st.nextToken());
- sg.setStartRes(Integer.parseInt(st.nextToken()) - 1);
- sg.setEndRes(Integer.parseInt(st.nextToken()) - 1);
+ 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"))
@@ -725,12 +1233,11 @@ public class AnnotationFile
}
}
-
-
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)
@@ -739,12 +1246,49 @@ public class AnnotationFile
}
}
+ 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
+ // 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;
@@ -770,6 +1314,8 @@ public class AnnotationFile
if (sg != null)
{
String keyValue, key, value;
+ ColourSchemeI def = sg.cs;
+ sg.cs = null;
while (st.hasMoreTokens())
{
keyValue = st.nextToken();
@@ -793,10 +1339,8 @@ public class AnnotationFile
{
sg.cs.setConservationInc(Integer.parseInt(value));
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(null),
- sg.getStartRes(),
- sg.getEndRes() + 1);
+ ResidueProperties.propHash, 3, sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, 25);
@@ -812,6 +1356,10 @@ public class AnnotationFile
{
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());
@@ -832,28 +1380,63 @@ public class AnnotationFile
{
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;
- while(st.hasMoreTokens())
+ 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();
- for(int i=0; i p)
+ {
+ sp.append(atos.substring(p, cp + 1));
+ }
+ else
+ {
+ sp.append(atos.substring(p));
+ sp.append(newline);
+ }
+ p = cp + 1;
+ } while (p > 0);
}
+ return sp.toString();
}
}