X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=7e2539f6aa1095e5d953e60a0ab3cdcbbccfb087;hb=94ca0419cc7afa75b3c51917a8beaf46a7c05540;hp=45e6c478c893e61a9f38fe36eeade22e7c535b1a;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 45e6c47..7e2539f 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -1,60 +1,78 @@
/*
- * 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 java.awt.Color;
+import java.io.BufferedReader;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+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.HiddenColumns;
+import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.ColorUtils;
public class AnnotationFile
{
- public AnnotationFile()
- {
- init();
- }
+ private static final String GRAPHLINE = "GRAPHLINE";
+
+ private static final String COMBINE = "COMBINE";
- /**
- * character used to write newlines
- */
protected String newline = System.getProperty("line.separator");
+ private StringBuffer text;
+
+ private SequenceI refSeq = null;
+
+ private String refSeqId = null;
+
+ private long nlinesread = 0;
+
+ private String lastread = "";
+
/**
- * set new line string and reset the output buffer
- *
- * @param nl
+ * Constructor
*/
- public void setNewlineString(String nl)
+ public AnnotationFile()
{
- newline = nl;
init();
}
- public String getNewlineString()
- {
- return newline;
- }
-
- StringBuffer text;
-
private void init()
{
text = new StringBuffer("JALVIEW_ANNOTATION" + newline + "# Created: "
@@ -64,18 +82,19 @@ 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 +104,22 @@ 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 HiddenColumns hiddencols;
- public Vector visibleGroups;
+ public final Hashtable hiddenRepSeqs;
- public Hashtable hiddenRepSeqs;
-
- public ViewDef(String viewname, HiddenSequences hidseqs,
- ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+ public ViewDef(String vname, HiddenSequences hseqs, HiddenColumns 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 +134,43 @@ public class AnnotationFile
* @return annotation file
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
- List list, Hashtable properties, ViewDef[] views)
+ List list, Hashtable properties, HiddenColumns 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");
+
+ String regions = cs.regionsToString(",", "-");
+ text.append(regions);
+ text.append("\n");
+ }
+ // TODO: allow efficient recovery of annotation data shown in several
+ // different views
if (annotations != null)
{
boolean oneColour = true;
@@ -131,7 +182,9 @@ 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;
@@ -139,7 +192,8 @@ public class AnnotationFile
{
row = annotations[i];
- if (!row.visible && !row.hasScore())
+ if (!row.visible && !row.hasScore() && !(row.graphGroup > -1
+ && graphGroupSeen.get(row.graphGroup)))
{
continue;
}
@@ -147,55 +201,15 @@ 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)
- {
+ writeGroup_Ref(refGroup, row.groupRef);
+ refGroup = row.groupRef;
- 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;
+ 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
@@ -204,14 +218,15 @@ public class AnnotationFile
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
+ && row.annotations[j].displayCharacter.length() > 0
+ && !row.annotations[j].displayCharacter.equals(" "));
+ hasGlyphs |= (row.annotations[j].secondaryStructure != 0
+ && row.annotations[j].secondaryStructure != ' ');
+ hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't
// be
// rendered..
- hasText |= (row.annotations[j].description != null && row.annotations[j].description
- .length() > 0);
+ hasText |= (row.annotations[j].description != null
+ && row.annotations[j].description.length() > 0);
}
}
@@ -244,20 +259,23 @@ public class AnnotationFile
graphLine.append("\t");
graphLine.append(row.getThreshold().label);
graphLine.append("\t");
- graphLine.append(jalview.util.Format.getHexString(row
- .getThreshold().colour));
+ graphLine.append(jalview.util.Format
+ .getHexString(row.getThreshold().colour));
graphLine.append(newline);
}
if (row.graphGroup > -1)
{
- String key = String.valueOf(row.graphGroup);
+ graphGroupSeen.set(row.graphGroup);
+ Integer key = Integer.valueOf(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);
}
}
@@ -293,13 +311,13 @@ 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.");
+ // jalview.bin.Console.errPrintln("Skipping NaN - not valid value.");
text.append(comma + 0f);// row.annotations[j].value);
}
comma = ",";
@@ -337,11 +355,8 @@ public class AnnotationFile
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 = ",";
}
}
@@ -349,7 +364,9 @@ public class AnnotationFile
}
if (row.hasScore())
+ {
text.append("\t" + row.score);
+ }
text.append(newline);
@@ -374,21 +391,40 @@ 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)
{
- text.append("COMBINE\t");
- Enumeration en = graphGroup.elements();
- while (en.hasMoreElements())
+ SequenceI oldRefSeq = refSeq;
+ SequenceGroup oldRefGroup = refGroup;
+ for (Map.Entry combine_statement : graphGroup
+ .entrySet())
{
- text.append(en.nextElement());
+ Object[] seqRefAndGroup = graphGroup_refs
+ .get(combine_statement.getKey());
+
+ writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]);
+ refSeq = (SequenceI) seqRefAndGroup[0];
+
+ writeGroup_Ref(refGroup, (SequenceGroup) seqRefAndGroup[1]);
+ refGroup = (SequenceGroup) seqRefAndGroup[1];
+ text.append("COMBINE\t");
+ text.append(combine_statement.getValue());
text.append(newline);
}
+ writeSequence_Ref(refSeq, oldRefSeq);
+ refSeq = oldRefSeq;
+
+ writeGroup_Ref(refGroup, oldRefGroup);
+ refGroup = oldRefGroup;
}
text.append(rowprops.toString());
}
@@ -413,13 +449,72 @@ 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)
@@ -465,7 +560,8 @@ 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)
{
@@ -539,54 +635,67 @@ public class AnnotationFile
}
}
- SequenceI refSeq = null;
+ public boolean annotateAlignmentView(AlignViewportI viewport, Object file,
+ DataSourceType protocol)
+ {
+ ColumnSelection colSel = viewport.getColumnSelection();
+ HiddenColumns hidden = viewport.getAlignment().getHiddenColumns();
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ if (hidden == null)
+ {
+ hidden = new HiddenColumns();
+ }
+ boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden, file,
+ protocol);
+ if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns()))
+ {
+ viewport.setColumnSelection(colSel);
+ viewport.getAlignment().setHiddenColumns(hidden);
+ }
- String refSeqId = null;
+ return rslt;
+ }
public boolean readAnnotationFile(AlignmentI al, String file,
- String protocol)
+ DataSourceType sourceType)
+ {
+ return readAnnotationFile(al, null, file, sourceType);
+ }
+
+ public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
+ Object file, DataSourceType sourceType)
{
BufferedReader in = null;
try
{
- if (protocol.equals(AppletFormatAdapter.FILE))
- {
- in = new BufferedReader(new FileReader(file));
- }
- else if (protocol.equals(AppletFormatAdapter.URL))
- {
- URL url = new URL(file);
- in = new BufferedReader(new InputStreamReader(url.openStream()));
- }
- else if (protocol.equals(AppletFormatAdapter.PASTE))
- {
- in = new BufferedReader(new StringReader(file));
- }
- else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
- {
- java.io.InputStream is = getClass().getResourceAsStream("/" + file);
- if (is != null)
- {
- in = new BufferedReader(new java.io.InputStreamReader(is));
- }
- }
+ in = new FileParse().getBufferedReader(file, sourceType);
if (in != null)
{
- return parseAnnotationFrom(al, in);
+ return parseAnnotationFrom(al, hidden, in);
}
-
} catch (Exception ex)
{
ex.printStackTrace();
- System.out.println("Problem reading annotation file: " + ex);
+ jalview.bin.Console.outPrintln("Problem reading annotation file: " + ex);
+ if (nlinesread > 0)
+ {
+ jalview.bin.Console.outPrintln("Last read line " + nlinesread + ": '" + lastread
+ + "' (first 80 chars) ...");
+ }
return false;
}
return false;
}
- public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
- throws Exception
+ public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,
+ BufferedReader in) throws Exception
{
+ nlinesread = 0;
+ ArrayList