X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FRedundancyPanel.java;h=3ff0ca3dcc453605c82507adb5de9e33e07aa843;hb=dfa04e77181fccfa6229ffef1591fc9c622d9b39;hp=1e51879561a099ea8171a69e428d2354e4b5f61a;hpb=fa93bb578999b13c0364a712ae368ca8841012a1;p=jalview.git diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java index 1e51879..3ff0ca3 100755 --- a/src/jalview/gui/RedundancyPanel.java +++ b/src/jalview/gui/RedundancyPanel.java @@ -1,20 +1,20 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; @@ -24,33 +24,41 @@ import java.awt.event.*; import javax.swing.*; import javax.swing.event.*; +import jalview.analysis.AlignSeq; import jalview.commands.*; import jalview.datamodel.*; import jalview.jbgui.*; -import jalview.util.*; +import jalview.util.MessageManager; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class RedundancyPanel - extends GSliderPanel implements Runnable +public class RedundancyPanel extends GSliderPanel implements Runnable { AlignFrame af; + AlignmentPanel ap; + Stack historyList = new Stack(); // simpler than synching with alignFrame. + float[] redundancy; + SequenceI[] originalSequences; + JInternalFrame frame; + Vector redundantSeqs; /** * Creates a new RedundancyPanel object. - * - * @param ap DOCUMENT ME! - * @param af DOCUMENT ME! + * + * @param ap + * DOCUMENT ME! + * @param af + * DOCUMENT ME! */ public RedundancyPanel(final AlignmentPanel ap, AlignFrame af) { @@ -67,7 +75,7 @@ public class RedundancyPanel } }); - applyButton.setText("Remove"); + applyButton.setText(MessageManager.getString("action.remove")); allGroupsCheck.setVisible(false); slider.setMinimum(0); slider.setMaximum(100); @@ -78,27 +86,28 @@ public class RedundancyPanel frame = new JInternalFrame(); frame.setContentPane(this); - Desktop.addInternalFrame(frame, "Redundancy threshold selection", 400, - 100, false); + Desktop.addInternalFrame(frame, MessageManager.getString("label.redundancy_threshold_selection"), 400, + 100, false); frame.addInternalFrameListener(new InternalFrameAdapter() { public void internalFrameClosing(InternalFrameEvent evt) { ap.idPanel.idCanvas.setHighlighted(null); } - } - ); + }); } /** - * This is a copy of remove redundancy in jalivew.datamodel.Alignment - * except we dont want to remove redundancy, just calculate once - * so we can use the slider to dynamically hide redundant sequences - * - * @param threshold DOCUMENT ME! - * @param sel DOCUMENT ME! - * + * This is a copy of remove redundancy in jalivew.datamodel.Alignment except + * we dont want to remove redundancy, just calculate once so we can use the + * slider to dynamically hide redundant sequences + * + * @param threshold + * DOCUMENT ME! + * @param sel + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public void run() @@ -107,7 +116,7 @@ public class RedundancyPanel progress.setIndeterminate(true); southPanel.add(progress, java.awt.BorderLayout.SOUTH); - label.setText("Calculating...."); + label.setText(MessageManager.getString("label.calculating")); slider.setVisible(false); applyButton.setEnabled(false); @@ -122,70 +131,26 @@ public class RedundancyPanel int start, end; - if ( (sg != null) && (sg.getSize() >= 1)) + 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) + if (ap.av.hasHiddenColumns()) { omitHidden = ap.av.getViewAsString(sg != null); } - - // 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 = Comparison.PID(seqi, seqj); - - if (seqj.length() < seqi.length()) - { - redundancy[j] = Math.max(pid, redundancy[j]); - } - else - { - redundancy[i] = Math.max(pid, redundancy[i]); - } - - } - } + redundancy = AlignSeq.computeRedundancyMatrix(originalSequences, + omitHidden, start, end, false); progress.setIndeterminate(false); progress.setVisible(false); @@ -227,8 +192,9 @@ public class RedundancyPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void applyButton_actionPerformed(ActionEvent e) { @@ -247,7 +213,8 @@ public class RedundancyPanel } } - // This has to be done before the restoreHistoryItem method of alignFrame will + // This has to be done before the restoreHistoryItem method of alignFrame + // will // actually restore these sequences. if (del.size() > 0) { @@ -264,16 +231,11 @@ public class RedundancyPanel } EditCommand cut = new EditCommand("Remove Redundancy", - EditCommand.CUT, deleted, 0, width, - ap.av.alignment); + EditCommand.CUT, deleted, 0, width, 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); + ap.av.getAlignment().deleteSequence(deleted[i]); if (sg != null) { sg.deleteSequence(deleted[i], false); @@ -284,16 +246,18 @@ public class RedundancyPanel 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()); } } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void undoButton_actionPerformed(ActionEvent e) { @@ -316,8 +280,9 @@ public class RedundancyPanel /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ public void valueField_actionPerformed(ActionEvent e) { @@ -325,8 +290,7 @@ public class RedundancyPanel { int i = Integer.parseInt(valueField.getText()); slider.setValue(i); - } - catch (Exception ex) + } catch (Exception ex) { valueField.setText(slider.getValue() + ""); }