+++ /dev/null
-/*
- * 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.
- *
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.workers;
-
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.seqfeatures.FeatureRenderer;
-import jalview.util.ColorUtils;
-import jalview.util.Comparison;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * A class to compute an alignment annotation with column counts of any
- * properties of interest of positions in an alignment. <br>
- * This is designed to be extensible, by supplying to the constructor an object
- * that computes a count for each residue position, based on the residue value
- * and any sequence features at that position.
- *
- */
-class ColumnCounterWorker extends AlignCalcWorker
-{
- FeatureCounterI counter;
-
- /**
- * Constructor registers the annotation for the given alignment frame
- *
- * @param af
- * @param counter
- */
- public ColumnCounterWorker(AlignViewportI viewport,
- AlignmentViewPanel panel, FeatureCounterI counter)
- {
- super(viewport, panel);
- ourAnnots = new ArrayList<AlignmentAnnotation>();
- this.counter = counter;
- calcMan.registerWorker(this);
- }
-
- /**
- * method called under control of AlignCalcManager to recompute the annotation
- * when the alignment changes
- */
- @Override
- public void run()
- {
- try
- {
- calcMan.notifyStart(this);
-
- while (!calcMan.notifyWorking(this))
- {
- try
- {
- Thread.sleep(200);
- } catch (InterruptedException ex)
- {
- ex.printStackTrace();
- }
- }
- if (alignViewport.isClosed())
- {
- abortAndDestroy();
- return;
- }
-
- if (alignViewport.getAlignment() != null)
- {
- try
- {
- computeAnnotations();
- } catch (IndexOutOfBoundsException x)
- {
- // probable race condition. just finish and return without any fuss.
- return;
- }
- }
- } catch (OutOfMemoryError error)
- {
- ap.raiseOOMWarning("calculating feature counts", error);
- calcMan.disableWorker(this);
- } finally
- {
- calcMan.workerComplete(this);
- }
-
- if (ap != null)
- {
- ap.adjustAnnotationHeight();
- ap.paintAlignment(true);
- }
-
- }
-
- /**
- * Scan each column of the alignment to calculate a count by feature type. Set
- * the count as the value of the alignment annotation for that feature type.
- */
- void computeAnnotations()
- {
- FeatureRenderer fr = new FeatureRenderer(alignViewport);
- // TODO use the commented out code once JAL-2075 is fixed
- // to get adequate performance on genomic length sequence
- AlignmentI alignment = alignViewport.getAlignment();
- // AlignmentView alignmentView = alignViewport.getAlignmentView(false);
- // AlignmentI alignment = alignmentView.getVisibleAlignment(' ');
-
- // int width = alignmentView.getWidth();
- int width = alignment.getWidth();
- int height = alignment.getHeight();
- int[] counts = new int[width];
- int max = 0;
-
- for (int col = 0; col < width; col++)
- {
- int count = 0;
- for (int row = 0; row < height; row++)
- {
- count += countFeaturesAt(alignment, col, row, fr);
- }
- counts[col] = count;
- max = Math.max(count, max);
- }
-
- Annotation[] anns = new Annotation[width];
- /*
- * add non-zero counts as annotations
- */
- for (int i = 0; i < counts.length; i++)
- {
- int count = counts[i];
- if (count > 0)
- {
- Color color = ColorUtils.getGraduatedColour(count, 0, Color.cyan,
- max, Color.blue);
- String str = String.valueOf(count);
- anns[i] = new Annotation(str, str, '0', count, color);
- }
- }
-
- /*
- * construct or update the annotation
- */
- AlignmentAnnotation ann = alignViewport.getAlignment()
- .findOrCreateAnnotation(counter.getName(),
- counter.getDescription(), false, null,
- null);
- ann.description = counter.getDescription();
- ann.showAllColLabels = true;
- ann.scaleColLabel = true;
- ann.graph = AlignmentAnnotation.BAR_GRAPH;
- ann.annotations = anns;
- setGraphMinMax(ann, anns);
- ann.validateRangeAndDisplay();
- if (!ourAnnots.contains(ann))
- {
- ourAnnots.add(ann);
- }
- }
-
- /**
- * Returns a count of any feature types present at the specified position of
- * the alignment
- *
- * @param alignment
- * @param col
- * @param row
- * @param fr
- */
- int countFeaturesAt(AlignmentI alignment, int col, int row,
- FeatureRenderer fr)
- {
- SequenceI seq = alignment.getSequenceAt(row);
- if (seq == null)
- {
- return 0;
- }
- if (col >= seq.getLength())
- {
- return 0;// sequence doesn't extend this far
- }
- char res = seq.getCharAt(col);
- if (Comparison.isGap(res))
- {
- return 0;
- }
- int pos = seq.findPosition(col);
-
- /*
- * compute a count for any displayed features at residue
- */
- // NB have to adjust pos if using AlignmentView.getVisibleAlignment
- // see JAL-2075
- List<SequenceFeature> features = fr.findFeaturesAtRes(seq, pos);
- int count = this.counter.count(String.valueOf(res), features);
- return count;
- }
-
- /**
- * Method called when the user changes display options that may affect how the
- * annotation is rendered, but do not change its values. Currently no such
- * options affect user-defined annotation, so this method does nothing.
- */
- @Override
- public void updateAnnotation()
- {
- // do nothing
- }
-
- /**
- * Answers true to indicate that if this worker's annotation is deleted from
- * the display, the worker should also be removed. This prevents it running
- * and recreating the annotation when the alignment changes.
- */
- @Override
- public boolean isDeletable()
- {
- return true;
- }
-}
git://source.jalview.org / jalview.git / blobdiff