X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRedundancyPanel.java;h=6be416c59ddddbee6d9bc979bc2df0ed9528badd;hb=7dc7fb2a35c435d825bc91c5ae60ec6073419a69;hp=0b4987c5eb112581a58f159c084893bff8ba3343;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java old mode 100755 new mode 100644 index 0b4987c..6be416c --- a/src/jalview/appletgui/RedundancyPanel.java +++ b/src/jalview/appletgui/RedundancyPanel.java @@ -1,29 +1,44 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * 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. - * + * 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 @@ -48,7 +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); @@ -58,17 +74,18 @@ public class RedundancyPanel extends SliderPanel implements Runnable, slider.addAdjustmentListener(new AdjustmentListener() { + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { - valueField.setText(slider.getValue() + ""); + valueField.setText(String.valueOf(slider.getValue())); sliderValueChanged(); } }); 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); @@ -88,9 +105,10 @@ public class RedundancyPanel extends SliderPanel implements Runnable, * * @return DOCUMENT ME! */ + @Override public void run() { - label.setText("Calculating...."); + label.setText(MessageManager.getString("label.calculating")); slider.setVisible(false); applyButton.setEnabled(false); @@ -120,61 +138,16 @@ public class RedundancyPanel extends SliderPanel implements Runnable, 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)); } @@ -187,23 +160,21 @@ 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); } + @Override public void applyButton_actionPerformed() { Vector del = new Vector(); @@ -238,13 +209,13 @@ public class RedundancyPanel extends SliderPanel implements Runnable, } } - EditCommand cut = new EditCommand("Remove Redundancy", - EditCommand.CUT, deleted, 0, width, ap.av.getAlignment()); - AlignmentI alignment=ap.av.getAlignment(); + 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++) { alignment.deleteSequence(deleted[i]); - PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true); if (sg != null) { sg.deleteSequence(deleted[i], false); @@ -255,21 +226,25 @@ public class RedundancyPanel extends SliderPanel implements Runnable, ap.alignFrame.addHistoryItem(cut); + PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true); ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() .getSequences()); } } + @Override public void undoButton_actionPerformed() { 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); @@ -292,31 +267,38 @@ public class RedundancyPanel extends SliderPanel implements Runnable, } } + @Override public void windowOpened(WindowEvent evt) { } + @Override public void windowClosing(WindowEvent evt) { ap.idPanel.idCanvas.setHighlighted(null); } + @Override public void windowClosed(WindowEvent evt) { } + @Override public void windowActivated(WindowEvent evt) { } + @Override public void windowDeactivated(WindowEvent evt) { } + @Override public void windowIconified(WindowEvent evt) { } + @Override public void windowDeiconified(WindowEvent evt) { }