X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=a81ffd49c08e2a960d6b114ebc8a7c017d1d3563;hb=49ff786d8e7d016cac6895539e6fb0eac8aae95c;hp=b3c6a01ccd6939e038c7544bca461ab94c012745;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java old mode 100755 new mode 100644 index b3c6a01..a81ffd4 --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -1,35 +1,48 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 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. - * + * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.commands.*; -import jalview.datamodel.*; +import jalview.analysis.AlignSeq; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.util.MessageManager; + +import java.awt.Frame; +import java.awt.event.ActionEvent; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.event.WindowEvent; +import java.awt.event.WindowListener; +import java.util.ArrayList; +import java.util.List; +import java.util.Stack; +import java.util.Vector; public class RedundancyPanel extends SliderPanel implements Runnable, WindowListener { - AlignmentPanel ap; - Stack historyList = new Stack(); // simpler than synching with alignFrame. float[] redundancy; @@ -50,7 +63,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable, applyButton.setVisible(true); allGroupsCheck.setVisible(false); - label.setText("Enter the redundancy threshold"); + label.setText(MessageManager + .getString("label.enter_redundancy_threshold")); valueField.setText("100"); slider.setVisibleAmount(1); @@ -69,8 +83,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable, frame = new Frame(); frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, - "Redundancy threshold selection", 400, 100); + jalview.bin.JalviewLite.addFrame(frame, MessageManager + .getString("label.redundancy_threshold_selection"), 400, 100); frame.addWindowListener(this); @@ -92,7 +106,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, */ public void run() { - label.setText("Calculating...."); + label.setText(MessageManager.getString("label.calculating")); slider.setVisible(false); applyButton.setEnabled(false); @@ -109,74 +123,29 @@ public class RedundancyPanel extends SliderPanel implements Runnable, if ((sg != null) && (sg.getSize() >= 1)) { - originalSequences = sg.getSequencesInOrder(ap.av.alignment); + originalSequences = sg.getSequencesInOrder(ap.av.getAlignment()); start = sg.getStartRes(); end = sg.getEndRes(); } else { - originalSequences = ap.av.alignment.getSequencesArray(); + originalSequences = ap.av.getAlignment().getSequencesArray(); start = 0; - end = ap.av.alignment.getWidth(); + end = ap.av.getAlignment().getWidth(); } height = originalSequences.length; - redundancy = new float[height]; - for (int i = 0; i < height; i++) - { - redundancy[i] = 0f; - } - - // if (ap.av.hasHiddenColumns) - { - // omitHidden = ap.av.getSelectionAsString(); - } - - // long start = System.currentTimeMillis(); - - float pid; - String seqi, seqj; - for (int i = 0; i < height; i++) - { - for (int j = 0; j < i; j++) - { - if (i == j) - { - continue; - } - - if (omitHidden == null) - { - seqi = originalSequences[i].getSequenceAsString(start, end); - seqj = originalSequences[j].getSequenceAsString(start, end); - } - else - { - seqi = omitHidden[i]; - seqj = omitHidden[j]; - } - - pid = jalview.util.Comparison.PID(seqi, seqj); - - if (seqj.length() < seqi.length()) - { - redundancy[j] = Math.max(pid, redundancy[j]); - } - else - { - redundancy[i] = Math.max(pid, redundancy[i]); - } - - } - } - - label.setText("Enter the redundancy threshold"); + redundancy = AlignSeq.computeRedundancyMatrix(originalSequences, + omitHidden, start, end, false); + label.setText(MessageManager + .getString("label.enter_redundancy_threshold")); slider.setVisible(true); applyButton.setEnabled(true); valueField.setVisible(true); validate(); + sliderValueChanged(); // System.out.println("blob done "+ (System.currentTimeMillis()-start)); } @@ -189,19 +158,16 @@ public class RedundancyPanel extends SliderPanel implements Runnable, float value = slider.getValue(); + List redundantSequences = new ArrayList(); for (int i = 0; i < redundancy.length; i++) { - if (value > redundancy[i]) - { - redundantSeqs.removeElement(originalSequences[i]); - } - else if (!redundantSeqs.contains(originalSequences[i])) + if (value <= redundancy[i]) { - redundantSeqs.addElement(originalSequences[i]); + redundantSequences.add(originalSequences[i]); } } - ap.idPanel.idCanvas.setHighlighted(redundantSeqs); + ap.idPanel.idCanvas.setHighlighted(redundantSequences); PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true); } @@ -240,13 +206,12 @@ public class RedundancyPanel extends SliderPanel implements Runnable, } } - EditCommand cut = new EditCommand("Remove Redundancy", - EditCommand.CUT, deleted, 0, width, ap.av.alignment); - + EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"), + Action.CUT, deleted, 0, width, ap.av.getAlignment()); + AlignmentI alignment = ap.av.getAlignment(); for (int i = 0; i < del.size(); i++) { - ap.av.alignment.deleteSequence(deleted[i]); - PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true); + alignment.deleteSequence(deleted[i]); if (sg != null) { sg.deleteSequence(deleted[i], false); @@ -257,8 +222,8 @@ public class RedundancyPanel extends SliderPanel implements Runnable, ap.alignFrame.addHistoryItem(cut); - ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() - .getSequences()); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true); + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences()); } } @@ -268,10 +233,11 @@ public class RedundancyPanel extends SliderPanel implements Runnable, CommandI command = (CommandI) historyList.pop(); command.undoCommand(null); - if (ap.av.historyList.contains(command)) + if (ap.av.getHistoryList().contains(command)) { - ap.av.historyList.removeElement(command); + ap.av.getHistoryList().remove(command); ap.alignFrame.updateEditMenuBar(); + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences()); } ap.paintAlignment(true);