/*
- * 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.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.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
+import java.awt.Color;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.InputStreamReader;
public String printAnnotations(AlignmentAnnotation[] annotations,
List<SequenceGroup> list, Hashtable properties)
{
- return printAnnotations(annotations, list, properties, null);
+ return printAnnotations(annotations, list, properties, null, null, null);
}
*/
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;
}
}
* @return annotation file
*/
public String printAnnotations(AlignmentAnnotation[] annotations,
- List<SequenceGroup> list, Hashtable properties, ViewDef[] views)
+ List<SequenceGroup> 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 (views != null)
+ 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())
{
- // are views defined and then annotation added to alignment or the other
- // way around ?
+ 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;
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<>();
+ Hashtable<Integer, Object[]> graphGroup_refs = new Hashtable<>();
BitSet graphGroupSeen = new BitSet();
java.awt.Color color;
&& 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 = ",";
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();
return false;
}
- public void printGroups(List<SequenceGroup> list)
+ protected void printGroups(List<SequenceGroup> list)
{
SequenceI seqrep = null;
for (SequenceGroup sg : list)
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)
{
String refSeqId = null;
public boolean annotateAlignmentView(AlignViewportI viewport,
- String file, String protocol)
+ String file, DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
+ HiddenColumns hidden = viewport.getAlignment().getHiddenColumns();
if (colSel == null)
{
colSel = new ColumnSelection();
}
- boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
+ if (hidden == null)
+ {
+ hidden = new HiddenColumns();
+ }
+ boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden,
file, protocol);
- if (rslt
- && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+ if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns()))
{
viewport.setColumnSelection(colSel);
+ viewport.getAlignment().setHiddenColumns(hidden);
}
return rslt;
}
+
public boolean readAnnotationFile(AlignmentI al, String file,
- String protocol)
+ DataSourceType sourceType)
{
- return readAnnotationFile(al, null, file, protocol);
+ return readAnnotationFile(al, null, file, sourceType);
}
- public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
- String file, String protocol)
+ public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
+ 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)
}
if (in != null)
{
- return parseAnnotationFrom(al, colSel, in);
+ return parseAnnotationFrom(al, hidden, in);
}
} catch (Exception ex)
private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
- public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
- BufferedReader in)
- throws Exception
+ public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,
+ BufferedReader in) throws Exception
{
nlinesread = 0;
- ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
- ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<Object[]>();
+ ArrayList<Object[]> combineAnnotation_calls = new ArrayList<>();
+ ArrayList<Object[]> deferredAnnotation_calls = new ArrayList<>();
boolean modified = false;
String groupRef = null;
Hashtable groupRefRows = new Hashtable();
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)
modified = true;
continue;
}
+ else if (token.equalsIgnoreCase("VIEW_HIDECOLS"))
+ {
+ if (st.hasMoreTokens())
+ {
+ if (hidden == null)
+ {
+ hidden = new HiddenColumns();
+ }
+ parseHideCols(hidden, st.nextToken());
+ }
+ modified = true;
+ continue;
+ }
else if (token.equalsIgnoreCase("HIDE_INSERTIONS"))
{
SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq;
}
if (sr != null)
{
- if (colSel == null)
+ if (hidden == null)
{
System.err
.println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
else
{
// consider deferring this till after the file has been parsed ?
- colSel.hideInsertionsFor(sr);
+ hidden.hideInsertionsFor(sr);
}
}
modified = true;
modified = true;
}
// Resolve the groupRefs
- Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<String, SequenceGroup>();
+ Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<>();
Enumeration en = groupRefRows.keys();
while (en.hasMoreElements())
(SequenceI) _deferred_args[2], // refSeq
(_deferred_args[3] == null) ? null : groupRefLookup
.get(_deferred_args[3]) // the reference
- // group, or null
+ // group, or null
);
}
}
(SequenceI) _combine_args[1], // refSeq
(_combine_args[2] == null) ? null : groupRefLookup
.get(_combine_args[2]) // the reference group,
- // or null
+ // or null
);
}
}
return modified;
}
+ private void parseHideCols(HiddenColumns hidden, 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)
+ {
+ hidden.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)
+ {
+ hidden.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;
}
}
}
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)
{
}
}
}
- 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 printAnnotations(viewport.isShowAnnotation() ? viewport
.getAlignment().getAlignmentAnnotation() : null, viewport
.getAlignment().getGroups(), viewport.getAlignment()
- .getProperties());
+ .getProperties(), viewport.getAlignment().getHiddenColumns(),
+ 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