X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=ef903e36a6af34ad2a4e67d6bb0f9a1b6d43e440;hb=e75847be3733978d2cd51d7121778e782ad0abf3;hp=3d42475fb3dfe765def8761c77bb28eef6777ee0;hpb=db7a726e4cf2c7d5f650085bd07b7f19254688e9;p=jalview.git
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 3d42475..ef903e3 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,29 +1,53 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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 .
+ * 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 java.io.*;
-import java.net.*;
-import java.util.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+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
{
@@ -64,18 +88,18 @@ public class AnnotationFile
}
/**
- * convenience method for pre-2.4 feature files which have no view, hidden
+ * 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 feature file as a string.
+ * @return annotation file as a string.
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
List list, Hashtable properties)
{
- return printAnnotations(annotations, list, properties, null);
+ return printAnnotations(annotations, list, properties, null, null, null);
}
@@ -85,23 +109,24 @@ public class AnnotationFile
*/
public class ViewDef
{
- public String viewname;
+ // TODO this class is not used - remove?
+ public final String viewname;
- public HiddenSequences hidseqs;
+ public final HiddenSequences hidseqs;
- public ColumnSelection hiddencols;
+ public final ColumnSelection hiddencols;
- public Vector visibleGroups;
+ // public final Vector visibleGroups;
- public Hashtable hiddenRepSeqs;
+ public final Hashtable hiddenRepSeqs;
- public ViewDef(String viewname, HiddenSequences hidseqs,
- ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+ public ViewDef(String vname, HiddenSequences hseqs,
+ ColumnSelection hcols, Hashtable hRepSeqs)
{
- this.viewname = viewname;
- this.hidseqs = hidseqs;
- this.hiddencols = hiddencols;
- this.hiddenRepSeqs = hiddenRepSeqs;
+ this.viewname = vname;
+ this.hidseqs = hseqs;
+ this.hiddencols = hcols;
+ this.hiddenRepSeqs = hRepSeqs;
}
}
@@ -116,10 +141,56 @@ public class AnnotationFile
* @return annotation file
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
- List list, Hashtable properties, ViewDef[] views)
+ List list, Hashtable properties,
+ ColumnSelection cs, AlignmentI al, ViewDef view)
{
- // TODO: resolve views issue : annotationFile could contain visible region,
- // or full data + hidden region specifications for a 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;
@@ -131,7 +202,8 @@ public class AnnotationFile
StringBuffer colours = new StringBuffer();
StringBuffer graphLine = new StringBuffer();
StringBuffer rowprops = new StringBuffer();
- Hashtable graphGroup = new Hashtable();
+ Hashtable graphGroup = new Hashtable();
+ Hashtable graphGroup_refs = new Hashtable();
BitSet graphGroupSeen = new BitSet();
java.awt.Color color;
@@ -140,7 +212,10 @@ public class AnnotationFile
{
row = annotations[i];
- if (!row.visible && !row.hasScore() && !(row.graphGroup>-1 && graphGroupSeen.get(row.graphGroup)))
+ if (!row.visible
+ && !row.hasScore()
+ && !(row.graphGroup > -1 && graphGroupSeen
+ .get(row.graphGroup)))
{
continue;
}
@@ -148,53 +223,12 @@ public class AnnotationFile
color = null;
oneColour = true;
- if (row.sequenceRef == null)
- {
- if (refSeq != null)
- {
- text.append(newline);
- text.append("SEQUENCE_REF\tALIGNMENT");
- text.append(newline);
- }
-
- refSeq = null;
- }
-
- 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 sequence references for the row
+ writeSequence_Ref(refSeq, row.sequenceRef);
+ refSeq = row.sequenceRef;
// 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);
- }
- }
+ 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.
@@ -208,7 +242,7 @@ public class AnnotationFile
&& 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
+ hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't
// be
// rendered..
hasText |= (row.annotations[j].description != null && row.annotations[j].description
@@ -253,13 +287,15 @@ public class AnnotationFile
if (row.graphGroup > -1)
{
graphGroupSeen.set(row.graphGroup);
- String key = String.valueOf(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);
}
}
@@ -295,13 +331,13 @@ public class AnnotationFile
}
if (hasValues)
{
- if (row.annotations[j].value != Float.NaN)
+ if (!Float.isNaN(row.annotations[j].value))
{
text.append(comma + row.annotations[j].value);
}
else
{
- System.err.println("Skipping NaN - not valid value.");
+ // System.err.println("Skipping NaN - not valid value.");
text.append(comma + 0f);// row.annotations[j].value);
}
comma = ",";
@@ -351,7 +387,9 @@ public class AnnotationFile
}
if (row.hasScore())
+ {
text.append("\t" + row.score);
+ }
text.append(newline);
@@ -376,21 +414,40 @@ public class AnnotationFile
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());
- text.append(graphLine.toString());
if (graphGroup.size() > 0)
{
- Enumeration en = graphGroup.elements();
- while (en.hasMoreElements())
+ 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(en.nextElement());
+ text.append(combine_statement.getValue());
text.append(newline);
}
+ writeSequence_Ref(refSeq, oldRefSeq);
+ refSeq = oldRefSeq;
+
+ writeGroup_Ref(refGroup, oldRefGroup);
+ refGroup = oldRefGroup;
}
text.append(rowprops.toString());
}
@@ -415,13 +472,72 @@ public class AnnotationFile
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();
}
- public void printGroups(List list)
+ private Object writeGroup_Ref(SequenceGroup refGroup,
+ SequenceGroup next_refGroup)
+ {
+ if (next_refGroup == null)
+ {
+
+ if (refGroup != null)
+ {
+ text.append(newline);
+ text.append("GROUP_REF\t");
+ text.append("ALIGNMENT");
+ text.append(newline);
+ }
+ return true;
+ }
+ else
+ {
+ if (refGroup == null || refGroup != next_refGroup)
+ {
+ text.append(newline);
+ text.append("GROUP_REF\t");
+ text.append(next_refGroup.getName());
+ text.append(newline);
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
+ {
+
+ if (next_refSeq == null)
+ {
+ if (refSeq != null)
+ {
+ text.append(newline);
+ text.append("SEQUENCE_REF\t");
+ text.append("ALIGNMENT");
+ text.append(newline);
+ return true;
+ }
+ }
+ else
+ {
+ if (refSeq == null || refSeq != next_refSeq)
+ {
+ text.append(newline);
+ text.append("SEQUENCE_REF\t");
+ text.append(next_refSeq.getName());
+ text.append(newline);
+ return true;
+ }
+ }
+ return false;
+ }
+
+ protected void printGroups(List list)
{
SequenceI seqrep = null;
for (SequenceGroup sg : list)
@@ -467,7 +583,8 @@ public class AnnotationFile
if (sg.cs != null)
{
text.append("colour=");
- text.append(ColourSchemeProperty.getColourName(sg.cs));
+ text.append(ColourSchemeProperty.getColourName(sg.cs
+ .getColourScheme()));
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
@@ -545,26 +662,50 @@ public class AnnotationFile
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,
- String protocol)
+ DataSourceType sourceType)
+ {
+ return readAnnotationFile(al, null, file, sourceType);
+ }
+
+ public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
+ String file, DataSourceType sourceType)
{
BufferedReader in = null;
try
{
- if (protocol.equals(AppletFormatAdapter.FILE))
+ if (sourceType == DataSourceType.FILE)
{
in = new BufferedReader(new FileReader(file));
}
- else if (protocol.equals(AppletFormatAdapter.URL))
+ else if (sourceType == DataSourceType.URL)
{
URL url = new URL(file);
in = new BufferedReader(new InputStreamReader(url.openStream()));
}
- else if (protocol.equals(AppletFormatAdapter.PASTE))
+ else if (sourceType == DataSourceType.PASTE)
{
in = new BufferedReader(new StringReader(file));
}
- else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+ else if (sourceType == DataSourceType.CLASSLOADER)
{
java.io.InputStream is = getClass().getResourceAsStream("/" + file);
if (is != null)
@@ -574,30 +715,35 @@ public class AnnotationFile
}
if (in != null)
{
- return parseAnnotationFrom(al, in);
+ 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) ...");
+ if (nlinesread > 0)
+ {
+ System.out.println("Last read line " + nlinesread + ": '"
+ + lastread + "' (first 80 chars) ...");
}
return false;
}
return false;
}
- long nlinesread=0;
- String lastread="";
- public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
- throws Exception
+
+ 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;
- /**
- * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
- */
- int combinecount = 0;
+ ArrayList