X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=b3b2111540fecc0a369da12f8d9dce01630bf5d1;hb=e015538903c8cabb2b90dd030e3e0c419a730db9;hp=01daf39a9f50ce55262a77af351c0ad1d352bc70;hpb=12b928f827972f429471a5bf7a832fa634259a16;p=jalview.git
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 01daf39..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);
}
@@ -78,13 +110,13 @@ public class AnnotationFile
* 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.
@@ -119,7 +151,9 @@ 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;
@@ -130,7 +164,10 @@ public class AnnotationFile
if (refSeq == null || refSeq != row.sequenceRef)
{
refSeq = row.sequenceRef;
- text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");
+ text.append(newline);
+ text.append("SEQUENCE_REF\t");
+ text.append(refSeq.getName());
+ text.append(newline);
}
}
// mark any group references for the row
@@ -139,7 +176,9 @@ public class AnnotationFile
if (refGroup != null)
{
- text.append("\nGROUP_REF\tALIGNMENT\n");
+ text.append(newline);
+ text.append("GROUP_REF\tALIGNMENT");
+ text.append(newline);
}
refGroup = null;
@@ -149,7 +188,10 @@ public class AnnotationFile
if (refGroup == null || refGroup != row.groupRef)
{
refGroup = row.groupRef;
- text.append("\nGROUP_REF\t" + refGroup.getName() + "\n");
+ text.append(newline);
+ text.append("GROUP_REF\t");
+ text.append(refGroup.getName());
+ text.append(newline);
}
}
@@ -195,16 +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)
@@ -309,25 +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)
{
- 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());
@@ -337,25 +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
@@ -364,13 +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"
@@ -381,61 +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())
{
@@ -448,9 +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);
}
}
@@ -462,13 +546,9 @@ public class AnnotationFile
public boolean readAnnotationFile(AlignmentI al, String file,
String protocol)
{
- String groupRef = null;
- Hashtable groupRefRows = new Hashtable();
-
- Hashtable autoAnnots = new Hashtable();
+ BufferedReader in = null;
try
{
- BufferedReader in = null;
if (protocol.equals(AppletFormatAdapter.FILE))
{
in = new BufferedReader(new FileReader(file));
@@ -490,7 +570,29 @@ 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;
@@ -509,14 +611,11 @@ public class AnnotationFile
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));
+ autoAnnots.put(
+ autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
+ (aa[aai].groupRef == null ? null
+ : aa[aai].groupRef.getName())),
+ new Integer(1));
}
}
}
@@ -565,22 +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;
}
@@ -645,17 +748,20 @@ 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;
}
@@ -728,15 +834,8 @@ public class AnnotationFile
annotation.score = score;
if (!overrideAutoAnnot
- && autoAnnots
- .containsKey(annotation.graph
- + "\t"
- + annotation.label
- + "\t"
- + annotation.description
- + "\t"
- + (refSeq != null ? refSeq
- .getDisplayId(true) : "")))
+ && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
+ groupRef)))
{
// skip - we've already got an automatic annotation of this type.
continue;
@@ -783,28 +882,28 @@ public class AnnotationFile
((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++)
+ for (SequenceGroup theGroup : al.getGroups())
{
- theGroup = (SequenceGroup) grps.elementAt(g);
if (theGroup.getName().equals(groupRef))
{
if (matched)
{
- // TODO: specify and implement duplication of alignment annotation for multiple group references.
+ // 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+"'");
+ + groupRef + "'");
}
else
{
@@ -824,26 +923,29 @@ public class AnnotationFile
}
((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
+ // do the
+ // glyph
+ // test
+ // if we
+ // don't
+ // want
+ // secondary
+ // structure
String desc = null, displayChar = null;
char ss = ' '; // secondaryStructure
float value = 0;
@@ -911,7 +1013,7 @@ public class AnnotationFile
}
}
if (hasSymbols
- && (token.equals("H") || token.equals("E") || token
+ && (token.equals("H") || token.equals("E") || token.equals("S") || token
.equals(" ")))
{
// Either this character represents a helix or sheet
@@ -982,45 +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()[i].label.equalsIgnoreCase(group))
- {
- graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;
- al.getAlignmentAnnotation()[i].graphGroup = graphGroup;
- break;
- }
- }
-
- // Now update groups
- while (st.hasMoreTokens())
+ 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;
@@ -1111,9 +1223,7 @@ public class AnnotationFile
}
else
{
- sg
- .addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),
- false);
+ sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
}
}
}
@@ -1153,13 +1263,16 @@ public class AnnotationFile
centerlab = Boolean.valueOf(value).booleanValue();
}
AlignmentAnnotation[] alr = al.getAlignmentAnnotation();
- for (int i = 0; i < alr.length; i++)
+ if (alr != null)
{
- if (alr[i].label.equalsIgnoreCase(label))
+ for (int i = 0; i < alr.length; i++)
{
- alr[i].centreColLabels = centerlab;
- alr[i].scaleColLabel = scaletofit;
- alr[i].showAllColLabels = showalllabs;
+ if (alr[i].label.equalsIgnoreCase(label))
+ {
+ alr[i].centreColLabels = centerlab;
+ alr[i].scaleColLabel = scaletofit;
+ alr[i].showAllColLabels = showalllabs;
+ }
}
}
}
@@ -1175,15 +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;
}
@@ -1221,11 +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);
@@ -1240,7 +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"))
{
@@ -1290,19 +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)
{
- aa = al.getAlignmentAnnotation()[i];
- if (aa.sequenceRef == refSeq && aa.label.equals(token))
+ System.err.print(" " + token);
+ }
+ else
+ {
+ 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)
@@ -1343,7 +1469,7 @@ public class AnnotationFile
else
{
sp.append(atos.substring(p));
- sp.append("\n");
+ sp.append(newline);
}
p = cp + 1;
} while (p > 0);