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.UserColourScheme;
+import jalview.util.ColorUtils;
+import java.awt.Color;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.BitSet;
import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
import java.util.Hashtable;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.StringTokenizer;
import java.util.Vector;
public String printAnnotations(AlignmentAnnotation[] annotations,
List<SequenceGroup> list, Hashtable properties)
{
- return printAnnotations(annotations, list, properties, null, null, 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,
- ColumnSelection cs, AlignmentI al, ViewDef view)
+ List<SequenceGroup> list, Hashtable properties, HiddenColumns cs,
+ AlignmentI al, ViewDef view)
{
if (view != null)
{
}
if (list == null)
{
- list = view.visibleGroups;
+ // list = view.visibleGroups;
}
if (cs == null)
{
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]);
- }
+
+ String regions = cs.regionsToString(",", "-");
+ text.append(regions);
text.append("\n");
}
// TODO: allow efficient recovery of annotation data shown in several
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[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;
}
writeGroup_Ref(refGroup, row.groupRef);
refGroup = row.groupRef;
- 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
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 != ' ');
+ && 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);
}
}
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.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 = ",";
}
}
for (Map.Entry<Integer, String> combine_statement : graphGroup
.entrySet())
{
- Object[] seqRefAndGroup = graphGroup_refs.get(combine_statement
- .getKey());
+ Object[] seqRefAndGroup = graphGroup_refs
+ .get(combine_statement.getKey());
writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]);
refSeq = (SequenceI) seqRefAndGroup[0];
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)
+ public boolean annotateAlignmentView(AlignViewportI viewport, 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,
- file, protocol);
- if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+ 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);
}
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)
System.out.println("Problem reading annotation file: " + ex);
if (nlinesread > 0)
{
- System.out.println("Last read line " + nlinesread + ": '"
- + lastread + "' (first 80 chars) ...");
+ System.out.println("Last read line " + nlinesread + ": '" + lastread
+ + "' (first 80 chars) ...");
}
return false;
}
private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
- public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
+ 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[]>();
+ List<Object[]> combineAnnotation_calls = new ArrayList<>();
+ List<Object[]> deferredAnnotation_calls = new ArrayList<>();
boolean modified = false;
String groupRef = null;
- Hashtable groupRefRows = new Hashtable();
-
- Hashtable autoAnnots = new Hashtable();
+ Map<String, Vector<AlignmentAnnotation>> groupRefRows = new HashMap<>();
+
+ Set<String> autoAnnots = new HashSet<>();
+ String line, label, description, token;
+ int graphStyle, index;
+ int refSeqIndex = 1;
+ int existingAnnotationCount = 0;
+ // when true - will add new rows regardless of whether they are duplicate
+ // auto-annotation like consensus or conservation graphs
+ boolean overrideAutoAnnot = false;
+ if (al.getAlignmentAnnotation() != null)
{
- String line, label, description, token;
- int graphStyle, index;
- int refSeqIndex = 1;
- int existingAnnotations = 0;
- // when true - will add new rows regardless of whether they are duplicate
- // auto-annotation like consensus or conservation graphs
- boolean overrideAutoAnnot = false;
- if (al.getAlignmentAnnotation() != null)
- {
- existingAnnotations = al.getAlignmentAnnotation().length;
- if (existingAnnotations > 0)
- {
- AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
- for (int aai = 0; aai < aa.length; aai++)
+ existingAnnotationCount = al.getAlignmentAnnotation().length;
+ if (existingAnnotationCount > 0)
+ {
+ AlignmentAnnotation[] aa = al.getAlignmentAnnotation();
+ for (int aai = 0; aai < aa.length; aai++)
+ {
+ if (aa[aai].autoCalculated)
{
- if (aa[aai].autoCalculated)
- {
- // make a note of the name and description
- autoAnnots.put(
- autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
- (aa[aai].groupRef == null ? null
- : aa[aai].groupRef.getName())),
- new Integer(1));
- }
+ // make a note of the name and description
+ autoAnnots.add(autoAnnotsKey(aa[aai], aa[aai].sequenceRef,
+ (aa[aai].groupRef == null ? null
+ : aa[aai].groupRef.getName())));
}
}
}
+ }
- int alWidth = al.getWidth();
+ int alWidth = al.getWidth();
- StringTokenizer st;
- Annotation[] annotations;
- AlignmentAnnotation annotation = null;
+ StringTokenizer st;
+ Annotation[] annotations;
+ AlignmentAnnotation annotation = null;
- // First confirm this is an Annotation file
- boolean jvAnnotationFile = false;
- while ((line = in.readLine()) != null)
+ // First confirm this is an Annotation file
+ boolean jvAnnotationFile = false;
+ while ((line = in.readLine()) != null)
+ {
+ nlinesread++;
+ lastread = new String(line);
+ if (line.indexOf("#") == 0)
{
- nlinesread++;
- lastread = new String(line);
- if (line.indexOf("#") == 0)
- {
- continue;
- }
-
- if (line.indexOf("JALVIEW_ANNOTATION") > -1)
- {
- jvAnnotationFile = true;
- break;
- }
+ continue;
}
- if (!jvAnnotationFile)
+ if (line.indexOf("JALVIEW_ANNOTATION") > -1)
{
- in.close();
- return false;
+ jvAnnotationFile = true;
+ break;
}
+ }
- while ((line = in.readLine()) != null)
+ if (!jvAnnotationFile)
+ {
+ in.close();
+ return false;
+ }
+
+ while ((line = in.readLine()) != null)
+ {
+ nlinesread++;
+ lastread = new String(line);
+ if (line.indexOf("#") == 0 || line.indexOf("JALVIEW_ANNOTATION") > -1
+ || line.length() == 0)
{
- nlinesread++;
- lastread = new String(line);
- if (line.indexOf("#") == 0
- || line.indexOf("JALVIEW_ANNOTATION") > -1
- || line.length() == 0)
- {
- continue;
- }
+ continue;
+ }
- st = new StringTokenizer(line, "\t");
- token = st.nextToken();
- if (token.equalsIgnoreCase("COLOUR"))
- {
- // TODO: use graduated colour def'n here too
- colourAnnotations(al, st.nextToken(), st.nextToken());
- modified = true;
- continue;
- }
+ st = new StringTokenizer(line, "\t");
+ token = st.nextToken();
+ if (token.equalsIgnoreCase("COLOUR"))
+ {
+ // TODO: use graduated colour def'n here too
+ colourAnnotations(al, st.nextToken(), st.nextToken());
+ modified = true;
+ continue;
+ }
- else if (token.equalsIgnoreCase(COMBINE))
- {
- // keep a record of current state and resolve groupRef at end
- combineAnnotation_calls
- .add(new Object[] { st, refSeq, groupRef });
- modified = true;
- continue;
- }
- else if (token.equalsIgnoreCase("ROWPROPERTIES"))
- {
- addRowProperties(al, st);
- modified = true;
- continue;
- }
- else if (token.equalsIgnoreCase(GRAPHLINE))
- {
- // resolve at end
- deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st,
- refSeq, groupRef });
- modified = true;
- continue;
- }
+ else if (token.equalsIgnoreCase(COMBINE))
+ {
+ // keep a record of current state and resolve groupRef at end
+ combineAnnotation_calls.add(new Object[] { st, refSeq, groupRef });
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase("ROWPROPERTIES"))
+ {
+ addRowProperties(al, st);
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase(GRAPHLINE))
+ {
+ // resolve at end
+ deferredAnnotation_calls
+ .add(new Object[]
+ { GRAPHLINE, st, refSeq, groupRef });
+ modified = true;
+ continue;
+ }
- else if (token.equalsIgnoreCase("SEQUENCE_REF"))
+ else if (token.equalsIgnoreCase("SEQUENCE_REF"))
+ {
+ if (st.hasMoreTokens())
{
- if (st.hasMoreTokens())
+ refSeq = al.findName(refSeqId = st.nextToken());
+ if (refSeq == null)
{
- refSeq = al.findName(refSeqId = st.nextToken());
- if (refSeq == null)
- {
- refSeqId = null;
- }
- try
- {
- refSeqIndex = Integer.parseInt(st.nextToken());
- if (refSeqIndex < 1)
- {
- refSeqIndex = 1;
- System.out
- .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
- }
- } catch (Exception ex)
+ refSeqId = null;
+ }
+ try
+ {
+ refSeqIndex = Integer.parseInt(st.nextToken());
+ if (refSeqIndex < 1)
{
refSeqIndex = 1;
+ System.out.println(
+ "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");
}
- }
- else
+ } catch (Exception ex)
{
- refSeq = null;
- refSeqId = null;
+ refSeqIndex = 1;
}
- continue;
}
- else if (token.equalsIgnoreCase("GROUP_REF"))
+ else
{
- // Group references could be forward or backwards, so they are
- // resolved after the whole file is read in
- groupRef = null;
- if (st.hasMoreTokens())
+ refSeq = null;
+ refSeqId = null;
+ }
+ continue;
+ }
+ else if (token.equalsIgnoreCase("GROUP_REF"))
+ {
+ // Group references could be forward or backwards, so they are
+ // resolved after the whole file is read in
+ groupRef = null;
+ if (st.hasMoreTokens())
+ {
+ groupRef = st.nextToken();
+ if (groupRef.length() < 1)
+ {
+ groupRef = null; // empty string
+ }
+ else
{
- groupRef = st.nextToken();
- if (groupRef.length() < 1)
+ if (groupRefRows.get(groupRef) == null)
{
- groupRef = null; // empty string
- }
- else
- {
- if (groupRefRows.get(groupRef) == null)
- {
- groupRefRows.put(groupRef, new Vector());
- }
+ groupRefRows.put(groupRef, new Vector<>());
}
}
- continue;
- }
- else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
- {
- addGroup(al, st);
- modified = true;
- continue;
}
+ continue;
+ }
+ else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))
+ {
+ addGroup(al, st);
+ modified = true;
+ continue;
+ }
- else if (token.equalsIgnoreCase("PROPERTIES"))
- {
- addProperties(al, st);
- modified = true;
- continue;
- }
+ else if (token.equalsIgnoreCase("PROPERTIES"))
+ {
+ addProperties(al, st);
+ modified = true;
+ continue;
+ }
- else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
+ else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))
+ {
+ setBelowAlignment(al, st);
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase("ALIGNMENT"))
+ {
+ addAlignmentDetails(al, st);
+ modified = true;
+ continue;
+ }
+ // else if (token.equalsIgnoreCase("VIEW_DEF"))
+ // {
+ // addOrSetView(al,st);
+ // modified = true;
+ // continue;
+ // }
+ else if (token.equalsIgnoreCase("VIEW_SETREF"))
+ {
+ if (refSeq != null)
{
- setBelowAlignment(al, st);
- modified = true;
- continue;
+ al.setSeqrep(refSeq);
}
- else if (token.equalsIgnoreCase("ALIGNMENT"))
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase("VIEW_HIDECOLS"))
+ {
+ if (st.hasMoreTokens())
{
- addAlignmentDetails(al, st);
- modified = true;
- continue;
- }
- // else if (token.equalsIgnoreCase("VIEW_DEF"))
- // {
- // addOrSetView(al,st);
- // modified = true;
- // continue;
- // }
- else if (token.equalsIgnoreCase("VIEW_SETREF"))
- {
- if (refSeq != null)
+ if (hidden == null)
{
- al.setSeqrep(refSeq);
+ hidden = new HiddenColumns();
}
- modified = true;
- continue;
+ parseHideCols(hidden, st.nextToken());
}
- else if (token.equalsIgnoreCase("VIEW_HIDECOLS"))
+ modified = true;
+ continue;
+ }
+ else if (token.equalsIgnoreCase("HIDE_INSERTIONS"))
+ {
+ SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq;
+ if (sr == null)
{
- if (st.hasMoreTokens())
- {
- if (colSel == null)
- {
- colSel = new ColumnSelection();
- }
- parseHideCols(colSel, st.nextToken());
- }
- modified = true;
- continue;
+ sr = al.getSequenceAt(0);
}
- else if (token.equalsIgnoreCase("HIDE_INSERTIONS"))
+ if (sr != null)
{
- SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq;
- if (sr == null)
+ if (hidden == null)
{
- sr = al.getSequenceAt(0);
+ System.err.println(
+ "Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
+ + line);
}
- if (sr != null)
+ else
{
- 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);
- }
+ // consider deferring this till after the file has been parsed ?
+ hidden.hideList(sr.getInsertions());
}
- modified = true;
- continue;
}
+ modified = true;
+ continue;
+ }
- // Parse out the annotation row
- graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
- label = st.nextToken();
-
- index = 0;
- annotations = new Annotation[alWidth];
- description = null;
- float score = Float.NaN;
+ // Parse out the annotation row
+ graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
+ label = st.nextToken();
- if (st.hasMoreTokens())
- {
- line = st.nextToken();
+ index = 0;
+ annotations = new Annotation[alWidth];
+ description = null;
+ float score = Float.NaN;
- if (line.indexOf("|") == -1)
- {
- description = line;
- if (st.hasMoreTokens())
- {
- line = st.nextToken();
- }
- }
+ if (st.hasMoreTokens())
+ {
+ line = st.nextToken();
+ if (line.indexOf("|") == -1)
+ {
+ description = line;
if (st.hasMoreTokens())
{
- // This must be the score
- score = Float.valueOf(st.nextToken()).floatValue();
+ line = st.nextToken();
}
+ }
- st = new StringTokenizer(line, "|", true);
+ if (st.hasMoreTokens())
+ {
+ // This must be the score
+ score = Float.valueOf(st.nextToken()).floatValue();
+ }
- boolean emptyColumn = true;
- boolean onlyOneElement = (st.countTokens() == 1);
+ st = new StringTokenizer(line, "|", true);
- while (st.hasMoreElements() && index < alWidth)
- {
- token = st.nextToken().trim();
+ boolean emptyColumn = true;
+ boolean onlyOneElement = (st.countTokens() == 1);
- if (onlyOneElement)
- {
- try
- {
- score = Float.valueOf(token).floatValue();
- break;
- } catch (NumberFormatException ex)
- {
- }
- }
+ while (st.hasMoreElements() && index < alWidth)
+ {
+ token = st.nextToken().trim();
- if (token.equals("|"))
+ if (onlyOneElement)
+ {
+ try
{
- if (emptyColumn)
- {
- index++;
- }
-
- emptyColumn = true;
- }
- else
+ score = Float.valueOf(token).floatValue();
+ break;
+ } catch (NumberFormatException ex)
{
- annotations[index++] = parseAnnotation(token, graphStyle);
- emptyColumn = false;
}
}
- }
-
- annotation = new AlignmentAnnotation(label, description,
- (index == 0) ? null : annotations, 0, 0, graphStyle);
-
- annotation.score = score;
- if (!overrideAutoAnnot
- && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,
- groupRef)))
- {
- // skip - we've already got an automatic annotation of this type.
- continue;
- }
- // otherwise add it!
- if (refSeq != null)
- {
-
- annotation.belowAlignment = false;
- // make a copy of refSeq so we can find other matches in the alignment
- SequenceI referedSeq = refSeq;
- do
+ if (token.equals("|"))
{
- // copy before we do any mapping business.
- // TODO: verify that undo/redo with 1:many sequence associated
- // annotations can be undone correctly
- AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
- annotation
- .createSequenceMapping(referedSeq, refSeqIndex, false);
- annotation.adjustForAlignment();
- referedSeq.addAlignmentAnnotation(annotation);
- al.addAnnotation(annotation);
- al.setAnnotationIndex(annotation,
- al.getAlignmentAnnotation().length
- - existingAnnotations - 1);
- if (groupRef != null)
+ if (emptyColumn)
{
- ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
+ index++;
}
- // and recover our virgin copy to use again if necessary.
- annotation = ann;
- } while (refSeqId != null
- && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);
+ emptyColumn = true;
+ }
+ else
+ {
+ annotations[index++] = parseAnnotation(token, graphStyle);
+ emptyColumn = false;
+ }
}
- else
+
+ }
+
+ annotation = new AlignmentAnnotation(label, description,
+ (index == 0) ? null : annotations, 0, 0, graphStyle);
+
+ annotation.score = score;
+ if (!overrideAutoAnnot && autoAnnots
+ .contains(autoAnnotsKey(annotation, refSeq, groupRef)))
+ {
+ // skip - we've already got an automatic annotation of this type.
+ continue;
+ }
+ // otherwise add it!
+ if (refSeq != null)
+ {
+
+ annotation.belowAlignment = false;
+ // make a copy of refSeq so we can find other matches in the alignment
+ SequenceI referedSeq = refSeq;
+ do
{
+ // copy before we do any mapping business.
+ // TODO: verify that undo/redo with 1:many sequence associated
+ // annotations can be undone correctly
+ AlignmentAnnotation ann = new AlignmentAnnotation(annotation);
+ annotation.createSequenceMapping(referedSeq, refSeqIndex, false);
+ annotation.adjustForAlignment();
+ referedSeq.addAlignmentAnnotation(annotation);
al.addAnnotation(annotation);
al.setAnnotationIndex(annotation,
- al.getAlignmentAnnotation().length - existingAnnotations
- - 1);
+ al.getAlignmentAnnotation().length
+ - existingAnnotationCount - 1);
if (groupRef != null)
{
- ((Vector) groupRefRows.get(groupRef)).addElement(annotation);
+ groupRefRows.get(groupRef).addElement(annotation);
}
+ // and recover our virgin copy to use again if necessary.
+ annotation = ann;
+
+ } while (refSeqId != null && (referedSeq = al.findName(referedSeq,
+ refSeqId, true)) != null);
+ }
+ else
+ {
+ al.addAnnotation(annotation);
+ al.setAnnotationIndex(annotation, al.getAlignmentAnnotation().length
+ - existingAnnotationCount - 1);
+ if (groupRef != null)
+ {
+ groupRefRows.get(groupRef).addElement(annotation);
}
- // and set modification flag
- modified = true;
}
- // Resolve the groupRefs
- Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<String, SequenceGroup>();
- Enumeration en = groupRefRows.keys();
+ // and set modification flag
+ modified = true;
+ }
+ // Resolve the groupRefs
+ Hashtable<String, SequenceGroup> groupRefLookup = new Hashtable<>();
+ Iterator<String> en = groupRefRows.keySet().iterator();
- while (en.hasMoreElements())
+ while (en.hasNext())
+ {
+ groupRef = en.next();
+ boolean matched = false;
+ // Resolve group: TODO: add a getGroupByName method to alignments
+ for (SequenceGroup theGroup : al.getGroups())
{
- groupRef = (String) en.nextElement();
- boolean matched = false;
- // Resolve group: TODO: add a getGroupByName method to alignments
- for (SequenceGroup theGroup : al.getGroups())
+ if (theGroup.getName().equals(groupRef))
{
- if (theGroup.getName().equals(groupRef))
+ if (matched)
{
- if (matched)
- {
- // TODO: specify and implement duplication of alignment annotation
- // for multiple group references.
- System.err
- .println("Ignoring 1:many group reference mappings for group name '"
- + groupRef + "'");
- }
- else
+ // TODO: specify and implement duplication of alignment annotation
+ // for multiple group references.
+ System.err.println(
+ "Ignoring 1:many group reference mappings for group name '"
+ + groupRef + "'");
+ }
+ else
+ {
+ matched = true;
+ Vector<AlignmentAnnotation> rowset = groupRefRows.get(groupRef);
+ groupRefLookup.put(groupRef, theGroup);
+ if (rowset != null && rowset.size() > 0)
{
- matched = true;
- Vector rowset = (Vector) groupRefRows.get(groupRef);
- groupRefLookup.put(groupRef, theGroup);
- if (rowset != null && rowset.size() > 0)
+ AlignmentAnnotation alan = null;
+ for (int elm = 0, elmSize = rowset
+ .size(); elm < elmSize; elm++)
{
- AlignmentAnnotation alan = null;
- for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)
- {
- alan = (AlignmentAnnotation) rowset.elementAt(elm);
- alan.groupRef = theGroup;
- }
+ alan = rowset.elementAt(elm);
+ alan.groupRef = theGroup;
}
}
}
}
- ((Vector) groupRefRows.get(groupRef)).removeAllElements();
- }
- // process any deferred attribute settings for each context
- for (Object[] _deferred_args : deferredAnnotation_calls)
- {
- if (_deferred_args[0] == GRAPHLINE)
- {
- addLine(al,
- (StringTokenizer) _deferred_args[1], // st
- (SequenceI) _deferred_args[2], // refSeq
- (_deferred_args[3] == null) ? null : groupRefLookup
- .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
- */
- int combinecount = 0;
- 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(_combine_args[2]) // the reference group,
- // or null
+ groupRefRows.get(groupRef).removeAllElements();
+ }
+ // process any deferred attribute settings for each context
+ for (Object[] _deferred_args : deferredAnnotation_calls)
+ {
+ if (_deferred_args[0] == GRAPHLINE)
+ {
+ addLine(al, (StringTokenizer) _deferred_args[1], // st
+ (SequenceI) _deferred_args[2], // refSeq
+ (_deferred_args[3] == null) ? null
+ : groupRefLookup.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
+ */
+ int combinecount = 0;
+ 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(_combine_args[2]) // the reference
+ // group,
+ // or null
+ );
+ }
+
return modified;
}
- private void parseHideCols(ColumnSelection colSel, String nextToken)
+ private void parseHideCols(HiddenColumns hidden, String nextToken)
{
StringTokenizer inval = new StringTokenizer(nextToken, ",");
while (inval.hasMoreTokens())
from = to = Integer.parseInt(range);
if (from >= 0)
{
- colSel.hideColumns(from, to);
+ hidden.hideColumns(from, to);
}
}
else
}
if (from > 0 && to >= from)
{
- colSel.hideColumns(from, to);
+ hidden.hideColumns(from, to);
}
}
}
}
- private Object autoAnnotsKey(AlignmentAnnotation annotation,
+ private String autoAnnotsKey(AlignmentAnnotation annotation,
SequenceI refSeq, String groupRef)
{
return annotation.graph + "\t" + annotation.label + "\t"
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
displayChar = token;
}
}
- if (hasSymbols
- && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
+ if (hasSymbols && (token.length() == 1
+ && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
.contains(token)))
{
// Either this character represents a helix or sheet
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;
}
}
}
}
else
{
- System.err
- .println("Couldn't combine annotations. None are added to alignment yet!");
+ System.err.println(
+ "Couldn't combine annotations. None are added to alignment yet!");
}
}
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)
}
} catch (Exception e)
{
- System.err
- .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+ System.err.println(
+ "Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"
+ rng + "' - assuming alignment width for group.");
// assume group is full width
sg.setStartRes(0);
}
else
{
- sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1), false);
+ sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),
+ false);
}
}
}
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);
+ // TODO need to notify colourscheme of view reference once it is
+ // available
+ sg.cs.setColourScheme(
+ ColourSchemeProperty.getColourScheme(null, al, value));
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
else if (key.equalsIgnoreCase("consThreshold"))
{
sg.cs.setConservationInc(Integer.parseInt(value));
- Conservation c = new Conservation("Group", 3,
- sg.getSequences(null), sg.getStartRes(),
- sg.getEndRes() + 1);
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
c.verdict(false, 25); // TODO: refer to conservation percent threshold
}
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);
}
}
}
AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();
if (ala == null)
{
- System.err
- .print("Warning - no annotation to set below for sequence associated annotation:");
+ System.err.print(
+ "Warning - no annotation to set below for sequence associated annotation:");
}
while (st.hasMoreTokens())
{
public String printAnnotationsForView(AlignViewportI viewport)
{
- return printAnnotations(viewport.isShowAnnotation() ? viewport
- .getAlignment().getAlignmentAnnotation() : null, viewport
- .getAlignment().getGroups(), viewport.getAlignment()
- .getProperties(), viewport.getColumnSelection(),
+ return printAnnotations(
+ viewport.isShowAnnotation()
+ ? viewport.getAlignment().getAlignmentAnnotation()
+ : null,
+ viewport.getAlignment().getGroups(),
+ viewport.getAlignment().getProperties(),
+ viewport.getAlignment().getHiddenColumns(),
viewport.getAlignment(), null);
}
git://source.jalview.org / jalview.git / blobdiff