X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=b3b2111540fecc0a369da12f8d9dce01630bf5d1;hb=e015538903c8cabb2b90dd030e3e0c419a730db9;hp=00b7ead85bde0ac4d6b5c104d33c3752c971904f;hpb=75a1f7cee379a690c42b5ac2c5f58c4475f46564;p=jalview.git
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 00b7ead..b3b2111 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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 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 file is part of Jalview.
*
- * 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.
+ * 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.
*
- * 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 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;
@@ -28,22 +27,55 @@ 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 list
* @param properties
* @return feature file as a string.
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
- Vector groups, Hashtable properties)
+ List list, Hashtable properties)
{
- return printAnnotations(annotations, groups, properties, null);
+ return printAnnotations(annotations, list, properties, null);
}
@@ -72,24 +104,29 @@ public class AnnotationFile
this.hiddenRepSeqs = hiddenRepSeqs;
}
}
+
/**
- * Prepare an annotation file given a set of annotations, groups, alignment properties and views.
+ * Prepare an annotation file given a set of annotations, groups, alignment
+ * properties and views.
+ *
* @param annotations
- * @param groups
+ * @param list
* @param properties
* @param views
* @return annotation file
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
- Vector groups, Hashtable properties, ViewDef[] views)
+ List list, Hashtable properties, ViewDef[] views)
{
- // TODO: resolve views issue : annotationFile could contain visible region, or full data + hidden region specifications for a view.
+ // 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();
@@ -114,18 +151,51 @@ public class AnnotationFile
{
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
+ {
+ 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
{
- refSeq = row.sequenceRef;
- text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
+ 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 = false, hasLabels = false, hasValues = false, hasText = false;
+
+ 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
@@ -138,8 +208,8 @@ public class AnnotationFile
.equals(" "));
hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't
- // be
- // rendered..
+ // be
+ // rendered..
hasText |= (row.annotations[j].description != null && row.annotations[j].description
.length() > 0);
}
@@ -167,16 +237,16 @@ public class AnnotationFile
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)
@@ -210,10 +280,15 @@ public class AnnotationFile
if (row.annotations[j] != null)
{
comma = "";
- if (hasGlyphs && 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 (hasValues)
@@ -276,24 +351,32 @@ public class AnnotationFile
if (row.hasScore())
text.append("\t" + row.score);
- text.append("\n");
+ text.append(newline);
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)
+ 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");
+ 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());
@@ -303,25 +386,31 @@ 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)
+ if (list != null)
{
- printGroups(groups);
+ printGroups(list);
}
if (properties != null)
{
- text.append("\n\nALIGNMENT");
+ text.append(newline);
+ text.append(newline);
+ text.append("ALIGNMENT");
Enumeration en = properties.keys();
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
@@ -330,13 +419,11 @@ public class AnnotationFile
return text.toString();
}
- public void printGroups(Vector sequenceGroups)
+ public void printGroups(List list)
{
- SequenceGroup sg;
SequenceI seqrep = null;
- for (int i = 0; i < sequenceGroups.size(); i++)
+ for (SequenceGroup sg:list)
{
- sg = (SequenceGroup) sequenceGroups.elementAt(i);
if (!sg.hasSeqrep())
{
text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"
@@ -347,61 +434,90 @@ public class AnnotationFile
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");
+ 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("showUnconserved=" + sg.getShowunconserved() + "\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 + "\t");
+ text.append("textColThreshold=");
+ text.append(sg.thresholdTextColour);
+ text.append("\t");
}
if (sg.idColour != null)
{
- text.append("idColour="
- + jalview.util.Format.getHexString(sg.idColour) + "\t");
+ text.append("idColour=");
+ text.append(jalview.util.Format.getHexString(sg.idColour));
+ text.append("\t");
}
if (sg.isHidereps())
{
@@ -414,9 +530,11 @@ public class AnnotationFile
if (seqrep != null)
{
// terminate the last line and clear the sequence ref for the group
- text.append("\nSEQUENCE_REF");
+ text.append(newline);
+ text.append("SEQUENCE_REF");
}
- text.append("\n\n");
+ text.append(newline);
+ text.append(newline);
}
}
@@ -428,9 +546,9 @@ public class AnnotationFile
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));
@@ -452,14 +570,55 @@ 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();
@@ -505,22 +664,26 @@ public class AnnotationFile
{
// 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;
}
@@ -554,7 +717,28 @@ public class AnnotationFile
}
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);
@@ -564,20 +748,24 @@ public class AnnotationFile
else if (token.equalsIgnoreCase("PROPERTIES"))
{
addProperties(al, st);
+ modified = true;
continue;
}
else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
{
setBelowAlignment(al, st);
+ modified = true;
continue;
}
else if (token.equalsIgnoreCase("ALIGNMENT"))
{
addAlignmentDetails(al, st);
+ modified = true;
continue;
}
+ // Parse out the annotation row
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
label = st.nextToken();
@@ -645,9 +833,17 @@ public class AnnotationFile
(index == 0) ? null : annotations, 0, 0, graphStyle);
annotation.score = score;
-
+ if (!overrideAutoAnnot
+ && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
+ groupRef)))
+ {
+ // 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;
@@ -665,6 +861,10 @@ public class AnnotationFile
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;
@@ -677,21 +877,75 @@ public class AnnotationFile
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();
+
+ while (en.hasMoreElements())
+ {
+ groupRef = (String) en.nextElement();
+ boolean matched = false;
+ // Resolve group: TODO: add a getGroupByName method to alignments
+ for (SequenceGroup theGroup : al.getGroups())
+ {
+ 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;
+ }
+
+ 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
+ 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;
@@ -706,7 +960,7 @@ public class AnnotationFile
UserColourScheme ucs = new UserColourScheme();
colour = ucs.getColourFromString(string.substring(i + 1, j));
- if ( i>0 && string.charAt(i-1)==',')
+ if (i > 0 && string.charAt(i - 1) == ',')
{
// clip the preceding comma as well
i--;
@@ -716,9 +970,11 @@ public class AnnotationFile
StringTokenizer st = new StringTokenizer(string, ",", true);
String token;
- boolean seenContent=false;
+ boolean seenContent = false;
+ int pass = 0;
while (st.hasMoreTokens())
{
+ pass++;
token = st.nextToken().trim();
if (token.equals(","))
{
@@ -730,7 +986,9 @@ public class AnnotationFile
}
seenContent = false;
continue;
- } else {
+ }
+ else
+ {
seenContent = true;
}
@@ -738,7 +996,7 @@ public class AnnotationFile
{
try
{
- displayChar = token;
+ displayChar = token;
// foo
value = new Float(token).floatValue();
parsedValue = true;
@@ -747,8 +1005,16 @@ public class AnnotationFile
{
}
}
-
- if (hasSymbols && (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
@@ -758,29 +1024,34 @@ public class AnnotationFile
displayChar = "";
}
}
- else if (desc == null)
+ else if (desc == null || (parsedValue && pass > 2))
{
desc = token;
}
}
-// if (!dcset && string.charAt(string.length() - 1) == ',')
-// {
-// displayChar = " "; // empty display char symbol.
-// }
- if (displayChar != null && 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;
+ }
+ }
}
- /*
- * In principle, this code will ensure that the Annotation element generated
- * is renderable by any of the applet or application rendering code but
- * instead we check for null strings when the display character is rendered.
- * if (displayChar==null) { displayChar=""; }
- */
Annotation anot = new Annotation(displayChar, desc, ss, value);
anot.colour = colour;
@@ -813,45 +1084,55 @@ 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() != null)
{
- 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))
{
+ 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;
@@ -942,9 +1223,7 @@ public class AnnotationFile
}
else
{
- sg
- .addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),
- false);
+ sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
}
}
}
@@ -964,22 +1243,28 @@ 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();
+ 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")) {
+ 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 (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))
@@ -989,8 +1274,10 @@ public class AnnotationFile
alr[i].showAllColLabels = showalllabs;
}
}
+ }
}
}
+
void addProperties(AlignmentI al, StringTokenizer st)
{
@@ -1001,15 +1288,12 @@ public class AnnotationFile
{
return;
}
- SequenceGroup sg = null;
-
+
String name = st.nextToken();
-
- Vector groups = al.getGroups();
- for (int i = 0; i < groups.size(); i++)
+ SequenceGroup sg=null;
+ for (SequenceGroup _sg:al.getGroups())
{
- sg = (SequenceGroup) groups.elementAt(i);
- if (sg.getName().equals(name))
+ if ((sg=_sg).getName().equals(name))
{
break;
}
@@ -1047,11 +1331,11 @@ 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);
+ c.verdict(false, 25); // TODO: refer to conservation percent threshold
sg.cs.setConservation(c);
@@ -1066,7 +1350,7 @@ public class AnnotationFile
}
else if (key.equalsIgnoreCase("showUnconserved"))
{
- sg.setShowunconserved(Boolean.valueOf(value).booleanValue());
+ sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());
}
else if (key.equalsIgnoreCase("displayText"))
{
@@ -1116,19 +1400,35 @@ public class AnnotationFile
void setBelowAlignment(AlignmentI al, StringTokenizer st)
{
String token;
- AlignmentAnnotation aa;
+ 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 < al.getAlignmentAnnotation().length; i++)
+ if (ala == null)
+ {
+ System.err.print(" " + token);
+ }
+ else
{
- aa = al.getAlignmentAnnotation()[i];
- if (aa.sequenceRef == refSeq && aa.label.equals(token))
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
- aa.belowAlignment = true;
+ 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)
@@ -1169,7 +1469,7 @@ public class AnnotationFile
else
{
sp.append(atos.substring(p));
- sp.append("\n");
+ sp.append(newline);
}
p = cp + 1;
} while (p > 0);