/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* 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.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
+
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.io.File;
+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
{
}
/**
- * 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<SequenceGroup> list, Hashtable properties)
{
- return printAnnotations(annotations, list, properties, null);
+ return printAnnotations(annotations, list, properties, null, null, null);
}
* @return annotation file
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
- List<SequenceGroup> list, Hashtable properties, ViewDef[] views)
+ List<SequenceGroup> 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<int[]> 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;
StringBuffer colours = new StringBuffer();
StringBuffer graphLine = new StringBuffer();
StringBuffer rowprops = new StringBuffer();
- Hashtable<Integer,String> graphGroup = new Hashtable<Integer,String>();
- Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer,Object[]>();
+ Hashtable<Integer, String> graphGroup = new Hashtable<Integer, String>();
+ Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<Integer, Object[]>();
BitSet graphGroupSeen = new BitSet();
java.awt.Color color;
{
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;
}
color = null;
oneColour = true;
-
+
// mark any sequence references for the row
- writeSequence_Ref(refSeq ,row.sequenceRef);
+ writeSequence_Ref(refSeq, row.sequenceRef);
refSeq = row.sequenceRef;
// mark any group references for the row
writeGroup_Ref(refGroup, row.groupRef);
&& 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
if (graphGroup.containsKey(key))
{
graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);
-
+
}
else
{
- graphGroup_refs.put(key, new Object[] { refSeq, refGroup});
+ graphGroup_refs.put(key, new Object[] { refSeq, refGroup });
graphGroup.put(key, row.label);
}
}
}
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 = ",";
}
if (row.hasScore())
+ {
text.append("\t" + row.score);
+ }
text.append(newline);
rowprops.append(row.centreColLabels);
rowprops.append(newline);
}
- if (graphLine.length()>0) {
+ if (graphLine.length() > 0)
+ {
text.append(graphLine.toString());
graphLine.setLength(0);
}
{
SequenceI oldRefSeq = refSeq;
SequenceGroup oldRefGroup = refGroup;
- for (Map.Entry<Integer, String> 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];
+ for (Map.Entry<Integer, String> 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(combine_statement.getValue());
text.append(newline);
}
writeSequence_Ref(refSeq, oldRefSeq);
refSeq = oldRefSeq;
-
+
writeGroup_Ref(refGroup, oldRefGroup);
refGroup = oldRefGroup;
}
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();
}
- private Object writeGroup_Ref(SequenceGroup refGroup, SequenceGroup next_refGroup)
+ private Object writeGroup_Ref(SequenceGroup refGroup,
+ SequenceGroup next_refGroup)
{
if (next_refGroup == null)
{
return true;
}
}
- return false;
+ return false;
}
-
+
private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq)
{
- if (next_refSeq==null)
+ if (next_refSeq == null)
{
if (refSeq != null)
{
if (sg.cs != null)
{
text.append("colour=");
- text.append(ColourSchemeProperty.getColourName(sg.cs));
+ text.append(sg.cs.toString());
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
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)
+ {
+ baseUri = "";
BufferedReader in = null;
try
{
- if (protocol.equals(AppletFormatAdapter.FILE))
+ if (sourceType == DataSourceType.FILE)
{
in = new BufferedReader(new FileReader(file));
+ baseUri = new File(file).getParent();
+ if (baseUri == null)
+ {
+ baseUri = "";
+ }
+ else
+ {
+ baseUri += "/";
+ }
}
- else if (protocol.equals(AppletFormatAdapter.URL))
+ else if (sourceType == DataSourceType.URL)
{
URL url = new URL(file);
in = new BufferedReader(new InputStreamReader(url.openStream()));
+ String bs = url.toExternalForm();
+ baseUri = bs.substring(0, bs.indexOf(url.getHost())
+ + url.getHost().length());
+ baseUri += url.toURI().getPath();
+ if (baseUri.lastIndexOf("/") > -1)
+ {
+ baseUri = baseUri.substring(0, baseUri.lastIndexOf("/")) + "/";
+ }
}
- else if (protocol.equals(AppletFormatAdapter.PASTE))
+ else if (sourceType == DataSourceType.PASTE)
{
in = new BufferedReader(new StringReader(file));
+ // TODO - support mimencoded PDBs for a paste.. ?
+ baseUri = "";
}
- else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+ else if (sourceType == DataSourceType.CLASSLOADER)
{
java.io.InputStream is = getClass().getResourceAsStream("/" + file);
if (is != null)
{
in = new BufferedReader(new java.io.InputStreamReader(is));
+ // TODO: this probably doesn't work for classloader - needs a test
+ baseUri = new File("/" + file).getParent() + "/";
}
}
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="";
- private static String GRAPHLINE="GRAPHLINE", COMBINE="COMBINE";
- public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
- throws Exception
+
+ long nlinesread = 0;
+
+ String lastread = "";
+
+ /**
+ * used for resolving absolute references to resources relative to
+ * annotationFile location
+ */
+ String baseUri = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE",
+ STRUCTMODEL = "STRUCTMODEL";
+
+ public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
+ BufferedReader in) throws Exception
{
nlinesread = 0;
ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
boolean jvAnnotationFile = false;
while ((line = in.readLine()) != null)
{
- nlinesread++;lastread = new String(line);
+ nlinesread++;
+ lastread = new String(line);
if (line.indexOf("#") == 0)
{
continue;
while ((line = in.readLine()) != null)
{
- nlinesread++;lastread = new String(line);
+ nlinesread++;
+ lastread = new String(line);
if (line.indexOf("#") == 0
|| line.indexOf("JALVIEW_ANNOTATION") > -1
|| line.length() == 0)
else if (token.equalsIgnoreCase(COMBINE))
{
// keep a record of current state and resolve groupRef at end
- combineAnnotation_calls.add(new Object[] { st, refSeq, groupRef});
+ combineAnnotation_calls
+ .add(new Object[] { st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase(GRAPHLINE))
{
// resolve at end
- deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st, refSeq, groupRef});
+ deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st,
+ refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
{
addGroup(al, st);
- modified=true;
+ modified = true;
continue;
}
modified = true;
continue;
}
-
+ // else if (token.equalsIgnoreCase("VIEW_DEF"))
+ // {
+ // addOrSetView(al,st);
+ // modified = true;
+ // continue;
+ // }
+ else if (token.equalsIgnoreCase("VIEW_SETREF"))
+ {
+ if (refSeq != null)
+ {
+ al.setSeqrep(refSeq);
+ }
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase("VIEW_HIDECOLS"))
+ {
+ if (st.hasMoreTokens())
+ {
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ parseHideCols(colSel, st.nextToken());
+ }
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase("HIDE_INSERTIONS"))
+ {
+ SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq;
+ if (sr == null)
+ {
+ sr = al.getSequenceAt(0);
+ }
+ if (sr != null)
+ {
+ if (colSel == null)
+ {
+ System.err
+ .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
+ + line);
+ }
+ else
+ {
+ // consider deferring this till after the file has been parsed ?
+ colSel.hideInsertionsFor(sr);
+ }
+ }
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase(STRUCTMODEL))
+ {
+ boolean failedtoadd = true;
+ // expect
+ // STRUCTMODEL <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile>
+ // <Confidence> <%.I.D>
+ // <MatchStart> <MatchEnd> <Coverage> [<Other Information>]
+ String querySeqId = !st.hasMoreTokens() ? "" : st.nextToken();
+ SequenceI querySeq = al.findName(querySeqId);
+ if (st.hasMoreTokens()) {
+ refSeq = al.findName(refSeqId = st.nextToken());
+ if (refSeq == null)
+ {
+ System.err.println("Couldn't locate " + refSeqId
+ + " in the alignment for STRUCTMODEL");
+ refSeqId = null;
+ }
+ else
+ {
+ String tempId = st.nextToken();
+ String fastaMapping = st.nextToken();
+ String confidence = !st.hasMoreTokens() ? "" : 100
+ * Double.valueOf(st.nextToken()) + "";
+ String pid = !st.hasMoreTokens() ? "" : st.nextToken();
+ String alignRange = !st.hasMoreTokens() ? "" : st.nextToken()
+ + "-" + st.nextToken();
+ String otherInfo = !st.hasMoreTokens() ? "" : st.nextToken();
+ String coverage = "";
+ if (add_structmodel(al, querySeq, refSeq, tempId,
+ fastaMapping,
+ alignRange, coverage,
+ confidence, pid, otherInfo))
+ {
+ failedtoadd = false;
+ }
+ }
+ }
+ if (failedtoadd)
+ {
+ System.err
+ .println("Need <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile> <Confidence> <%.I.D> <MatchStart> <MatchEnd> <Coverage> [<Other Information>] as tab separated fields after"
+ + STRUCTMODEL
+ + ".\nNote: other information could be provided in html format ");
+ } else {
+ modified = true;
+ }
+ continue;
+ }
// Parse out the annotation row
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
label = st.nextToken();
{
description = line;
if (st.hasMoreTokens())
+ {
line = st.nextToken();
+ }
}
if (st.hasMoreTokens())
modified = true;
}
// Resolve the groupRefs
- Hashtable <String,SequenceGroup> groupRefLookup=new Hashtable<String,SequenceGroup>();
+ Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<String, SequenceGroup>();
Enumeration en = groupRefRows.keys();
while (en.hasMoreElements())
{
matched = true;
Vector rowset = (Vector) groupRefRows.get(groupRef);
- groupRefLookup.put(groupRef, theGroup);
+ groupRefLookup.put(groupRef, theGroup);
if (rowset != null && rowset.size() > 0)
{
AlignmentAnnotation alan = null;
(StringTokenizer) _deferred_args[1], // st
(SequenceI) _deferred_args[2], // refSeq
(_deferred_args[3] == null) ? null : groupRefLookup
- .get((String) _deferred_args[3]) // the reference
- // group, or null
+ .get(_deferred_args[3]) // the reference
+ // group, or null
);
}
- }
+ }
// finally, combine all the annotation rows within each context.
/**
- * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones
+ * number of combine statements in this annotation file. Used to create
+ * new groups for combined annotation graphs without disturbing existing
+ * ones
*/
int combinecount = 0;
- for (Object[] _combine_args:combineAnnotation_calls) {
- combineAnnotations(al,
+ for (Object[] _combine_args : combineAnnotation_calls)
+ {
+ combineAnnotations(al,
++combinecount,
(StringTokenizer) _combine_args[0], // st
(SequenceI) _combine_args[1], // refSeq
- (_combine_args[2]==null) ? null : groupRefLookup.get((String)_combine_args[2]) // the reference group, or null
- );
+ (_combine_args[2] == null) ? null : groupRefLookup
+ .get(_combine_args[2]) // the reference group,
+ // or null
+ );
}
}
return modified;
}
+ /**
+ * resolve a structural model and generate and add an alignment sequence for
+ * it
+ *
+ * @param refSeq2
+ * @param tempId
+ * @param urlToModel
+ * @param urlToPairwise
+ * @return true if model and sequence was added
+ */
+ private boolean add_structmodel(AlignmentI al, SequenceI querySequence,
+ SequenceI templateSeq,
+ String modelFile, String fastaFile, String aRange,
+ String coverage, String confidence,
+ String pid, String otherInfo)
+ {
+ String warningMessage = null;
+ boolean added = false;
+ try {
+ String structureModelFile = resolveAbsolute(modelFile);
+ String fastaMappingFile = resolveAbsolute(fastaFile.replaceAll(
+ ".fasta.jal", ".fasta"));
+ // System.out.println("Model File >> " + structureModelFile);
+ // System.out.println("Fasta File >> " + fastaMappingFile);
+ PDBEntry phyre2PDBEntry = new PDBEntry(modelFile, null, Type.FILE,
+ structureModelFile);
+ String phyre2ModelDesc = generatePhyre2InfoHTMLTable(aRange,
+ coverage, confidence, pid, otherInfo);
+ phyre2PDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
+ templateSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ if (querySequence != null)
+ {
+ querySequence.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ }
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerPhyre2Template(structureModelFile, fastaMappingFile);
+ added = true;
+
+ } catch (Exception x)
+ {
+ warningMessage = x.toString();
+ } finally {
+ if (warningMessage !=null)
+ {
+ System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage);
+ }
+ }
+ return added;
+ }
+
+ private String generatePhyre2InfoHTMLTable(String aRange,
+ String coverage, String confidence, String pid, String otherInfo)
+ {
+ StringBuilder phyre2InfoBuilder = new StringBuilder();
+ phyre2InfoBuilder.append("<html><table border=\"1\" width=100%>");
+ phyre2InfoBuilder
+ .append("<tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr>");
+ if (aRange != null && !aRange.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Aligned range")
+ .append("</td><td>").append(aRange).append("</td></tr>");
+ }
+ if (coverage != null && !coverage.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Coverage")
+ .append("</td><td>").append(coverage).append("</td></tr>");
+ }
+ if (confidence != null && !confidence.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Confidence")
+ .append("</td><td>").append(confidence).append("</td></tr>");
+ }
+ if (pid != null && !pid.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("%.i.d")
+ .append("</td><td>").append(pid).append("</td></tr>");
+ }
+ if (otherInfo != null && !otherInfo.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Other information")
+ .append("</td><td>").append(otherInfo).append("</td></tr>");
+ }
+ phyre2InfoBuilder.append("</table></html>");
+ return phyre2InfoBuilder.toString();
+ }
+
+ private String resolveAbsolute(String relURI)
+ {
+ if (relURI.indexOf(":/") > -1 || relURI.startsWith("/")
+ || "".equals(baseUri) || relURI.startsWith(baseUri))
+ {
+ return relURI;
+ }
+ return baseUri + relURI;
+ }
+
+ private void parseHideCols(ColumnSelection colSel, String nextToken)
+ {
+ StringTokenizer inval = new StringTokenizer(nextToken, ",");
+ while (inval.hasMoreTokens())
+ {
+ String range = inval.nextToken().trim();
+ int from, to = range.indexOf("-");
+ if (to == -1)
+ {
+ from = to = Integer.parseInt(range);
+ if (from >= 0)
+ {
+ colSel.hideColumns(from, to);
+ }
+ }
+ else
+ {
+ from = Integer.parseInt(range.substring(0, to));
+ if (to < range.length() - 1)
+ {
+ to = Integer.parseInt(range.substring(to + 1));
+ }
+ else
+ {
+ to = from;
+ }
+ if (from > 0 && to >= from)
+ {
+ colSel.hideColumns(from, to);
+ }
+ }
+ }
+ }
+
private Object autoAnnotsKey(AlignmentAnnotation annotation,
SequenceI refSeq, String groupRef)
{
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
+ // don't do the glyph test if we don't want secondary structure
+ boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH);
String desc = null, displayChar = null;
char ss = ' '; // secondaryStructure
float value = 0;
boolean parsedValue = false, dcset = false;
// find colour here
- java.awt.Color colour = null;
+ Color colour = null;
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));
+ colour = ColorUtils.parseColourString(string.substring(i + 1,
+ j));
if (i > 0 && string.charAt(i - 1) == ',')
{
// clip the preceding comma as well
}
}
if (hasSymbols
- && (token.equals("H") || token.equals("E")
- || token.equals("S") || token.equals(" ")))
+ && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
+ .contains(token)))
{
// Either this character represents a helix or sheet
// or an integer which can be displayed
void colourAnnotations(AlignmentI al, String label, String colour)
{
- UserColourScheme ucs = new UserColourScheme(colour);
+ Color awtColour = ColorUtils.parseColourString(colour);
Annotation[] annotations;
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
{
if (annotations[j] != null)
{
- annotations[j].colour = ucs.findColour('A');
+ annotations[j].colour = awtColour;
}
}
}
}
}
- void combineAnnotations(AlignmentI al, int combineCount, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
+ void combineAnnotations(AlignmentI al, int combineCount,
+ StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
{
String group = st.nextToken();
// First make sure we are not overwriting the graphIndex
- int graphGroup=0;
+ int graphGroup = 0;
if (al.getAlignmentAnnotation() != null)
{
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
-
- if (aa.graphGroup>graphGroup)
+
+ if (aa.graphGroup > graphGroup)
{
// try to number graphGroups in order of occurence.
- graphGroup=aa.graphGroup+1;
+ graphGroup = aa.graphGroup + 1;
}
- if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
+ if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
+ && aa.label.equalsIgnoreCase(group))
{
- if (aa.graphGroup>-1)
+ if (aa.graphGroup > -1)
{
graphGroup = aa.graphGroup;
- } else {
+ }
+ else
+ {
if (graphGroup <= combineCount)
{
- graphGroup=combineCount+1;
+ graphGroup = combineCount + 1;
}
aa.graphGroup = graphGroup;
}
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
- if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group))
+ if (aa.sequenceRef == seqRef && aa.groupRef == groupRef
+ && aa.label.equalsIgnoreCase(group))
{
aa.graphGroup = graphGroup;
break;
}
}
- void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef)
+ void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef,
+ SequenceGroup groupRef)
{
String group = st.nextToken();
- AlignmentAnnotation annotation = null, alannot[] = al
- .getAlignmentAnnotation();
- float value = new Float(st.nextToken()).floatValue();
+ AlignmentAnnotation[] alannot = al.getAlignmentAnnotation();
+ String nextToken = st.nextToken();
+ float value = 0f;
+ try
+ {
+ value = Float.valueOf(nextToken);
+ } catch (NumberFormatException e)
+ {
+ System.err.println("line " + nlinesread + ": Threshold '" + nextToken
+ + "' invalid, setting to zero");
+ }
String label = st.hasMoreTokens() ? st.nextToken() : null;
- java.awt.Color colour = null;
+ Color colour = null;
if (st.hasMoreTokens())
{
- UserColourScheme ucs = new UserColourScheme(st.nextToken());
- colour = ucs.findColour('A');
+ colour = ColorUtils.parseColourString(st.nextToken());
}
if (alannot != null)
{
for (int i = 0; i < alannot.length; i++)
{
- if (alannot[i].label.equalsIgnoreCase(group) && (seqRef==null || alannot[i].sequenceRef==seqRef) && (groupRef==null || alannot[i].groupRef==groupRef))
+ if (alannot[i].label.equalsIgnoreCase(group)
+ && (seqRef == null || alannot[i].sequenceRef == seqRef)
+ && (groupRef == null || alannot[i].groupRef == groupRef))
{
alannot[i].setThreshold(new GraphLine(value, label, colour));
}
}
}
- if (annotation == null)
- {
- return;
- }
}
void addGroup(AlignmentI al, StringTokenizer st)
if (sg != null)
{
String keyValue, key, value;
- ColourSchemeI def = sg.cs;
- sg.cs = null;
+ ColourSchemeI def = sg.getColourScheme();
while (st.hasMoreTokens())
{
keyValue = st.nextToken();
}
else if (key.equalsIgnoreCase("colour"))
{
- sg.cs = ColourSchemeProperty.getColour(al, value);
+ sg.cs.setColourScheme(ColourSchemeProperty
+ .getColourScheme(al, value));
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
else if (key.equalsIgnoreCase("consThreshold"))
{
sg.cs.setConservationInc(Integer.parseInt(value));
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
+ Conservation c = new Conservation("Group", sg.getSequences(null),
sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
}
else if (key.equalsIgnoreCase("outlineColour"))
{
- sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+ sg.setOutlineColour(ColorUtils.parseColourString(value));
}
else if (key.equalsIgnoreCase("displayBoxes"))
{
}
else if (key.equalsIgnoreCase("textCol1"))
{
- sg.textColour = new UserColourScheme(value).findColour('A');
+ sg.textColour = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textCol2"))
{
- sg.textColour2 = new UserColourScheme(value).findColour('A');
+ sg.textColour2 = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textColThreshold"))
{
}
else if (key.equalsIgnoreCase("idColour"))
{
- // consider warning if colour doesn't resolve to a real colour
- sg.setIdColour((def = new UserColourScheme(value))
- .findColour('A'));
+ Color idColour = ColorUtils.parseColourString(value);
+ sg.setIdColour(idColour == null ? Color.black : idColour);
}
else if (key.equalsIgnoreCase("hide"))
{
}
sg.recalcConservation();
}
- if (sg.cs == null)
+ if (sg.getColourScheme() == null)
{
- sg.cs = def;
+ sg.setColourScheme(def);
}
}
}
*/
public String printCSVAnnotations(AlignmentAnnotation[] annotations)
{
+ if (annotations == null)
+ {
+ return "";
+ }
StringBuffer sp = new StringBuffer();
for (int i = 0; i < annotations.length; i++)
{
}
return sp.toString();
}
+
+ public String printAnnotationsForView(AlignViewportI viewport)
+ {
+ return printAnnotations(viewport.isShowAnnotation() ? viewport
+ .getAlignment().getAlignmentAnnotation() : null, viewport
+ .getAlignment().getGroups(), viewport.getAlignment()
+ .getProperties(), viewport.getColumnSelection(),
+ viewport.getAlignment(), null);
+ }
+
+ public String printAnnotationsForAlignment(AlignmentI al)
+ {
+ return printAnnotations(al.getAlignmentAnnotation(), al.getGroups(),
+ al.getProperties(), null, al, null);
+ }
}