/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
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.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
+
+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
{
}
/**
- * 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;
&& 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
}
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);
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();
String refSeqId = null;
+ public boolean annotateAlignmentView(AlignViewportI viewport,
+ String file, String 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)
{
+ return readAnnotationFile(al, null, file, protocol);
+ }
+
+ public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
+ String file, String protocol)
+ {
BufferedReader in = null;
try
{
}
if (in != null)
{
- return parseAnnotationFrom(al, in);
+ return parseAnnotationFrom(al, colSel, in);
}
} catch (Exception ex)
private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
- public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)
- throws Exception
+ public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
+ BufferedReader in) throws Exception
{
nlinesread = 0;
ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
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;
}
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;
+ }
// Parse out the annotation row
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
{
description = line;
if (st.hasMoreTokens())
+ {
line = st.nextToken();
+ }
}
if (st.hasMoreTokens())
(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
);
}
}
(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
+ .get(_combine_args[2]) // the reference group,
+ // or null
);
}
}
return modified;
}
+ 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)
{
}
}
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
}
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);
+ }
}
git://source.jalview.org / jalview.git / blobdiff