/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
+import jalview.util.Comparison;
+import jalview.util.Format;
import java.io.BufferedReader;
import java.io.FileReader;
}
/**
- * convenience method for pre-2.9 annotation files which have no view, hidden
- * columns or hidden row keywords.
+ * convenience method for pre-2.8.3 annotation files which have no view,
+ * hidden columns or hidden row keywords.
*
* @param annotations
* @param list
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 (views != null)
+ if (view != null)
{
- // are views defined and then annotation added to alignment or the other
- // way around ?
-
+ 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;
graphLine.append("\t");
graphLine.append(row.getThreshold().label);
graphLine.append("\t");
- graphLine.append(jalview.util.Format.getHexString(row
- .getThreshold().colour));
+ graphLine
+ .append(Format.getHexString(row.getThreshold().colour));
graphLine.append(newline);
}
&& j < row.annotations.length; j++)
{
if (refSeq != null
- && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
+ && Comparison.isGap(refSeq.getCharAt(j)))
{
continue;
}
{
text.append(comma
+ "["
- + jalview.util.Format
+ + Format
.getHexString(row.annotations[j].colour)
+ "]");
comma = ",";
colours.append("COLOUR\t");
colours.append(row.label);
colours.append("\t");
- colours.append(jalview.util.Format.getHexString(color));
+ colours.append(Format.getHexString(color));
colours.append(newline);
}
if (row.scaleColLabel || row.showAllColLabels
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();
}
}
text.append("outlineColour=");
- text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
+ text.append(Format.getHexString(sg.getOutlineColour()));
text.append("\t");
text.append("displayBoxes=");
if (sg.textColour != java.awt.Color.black)
{
text.append("textCol1=");
- text.append(jalview.util.Format.getHexString(sg.textColour));
+ text.append(Format.getHexString(sg.textColour));
text.append("\t");
}
if (sg.textColour2 != java.awt.Color.white)
{
text.append("textCol2=");
- text.append(jalview.util.Format.getHexString(sg.textColour2));
+ text.append(Format.getHexString(sg.textColour2));
text.append("\t");
}
if (sg.thresholdTextColour != 0)
if (sg.idColour != null)
{
text.append("idColour=");
- text.append(jalview.util.Format.getHexString(sg.idColour));
+ text.append(Format.getHexString(sg.idColour));
text.append("\t");
}
if (sg.isHidereps())
modified = true;
continue;
}
+ // else if (token.equalsIgnoreCase("VIEW_DEF"))
+ // {
+ // addOrSetView(al,st);
+ // modified = true;
+ // continue;
+ // }
else if (token.equalsIgnoreCase("VIEW_SETREF"))
{
if (refSeq != null)
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;
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)
{
return printAnnotations(viewport.isShowAnnotation() ? viewport
.getAlignment().getAlignmentAnnotation() : null, viewport
.getAlignment().getGroups(), viewport.getAlignment()
- .getProperties());
+ .getProperties(), viewport.getColumnSelection(),
+ viewport.getAlignment(), null);
}
public String printAnnotationsForAlignment(AlignmentI al)
{
return printAnnotations(al.getAlignmentAnnotation(), al.getGroups(),
- al.getProperties());
+ al.getProperties(), null, al, null);
}
}
git://source.jalview.org / jalview.git / blobdiff