X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColumnChooser.java;fp=src%2Fjalview%2Fappletgui%2FAnnotationColumnChooser.java;h=b4c1d54dabea6c3d29ee229b3441a06567dbfb32;hb=9f70ff4b6d193b340031997634c9e3602486bc8e;hp=a8dff62e59045a0abb18408d4bda11ac2d0709c3;hpb=76844c43faeeeba369deaf42f1998ca0fb33d956;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java index a8dff62..b4c1d54 100644 --- a/src/jalview/appletgui/AnnotationColumnChooser.java +++ b/src/jalview/appletgui/AnnotationColumnChooser.java @@ -21,7 +21,7 @@ package jalview.appletgui; import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.schemes.AnnotationColourGradient; import jalview.util.MessageManager; import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; @@ -46,7 +46,7 @@ import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.TextEvent; import java.awt.event.TextListener; -import java.util.Iterator; +import java.util.ArrayList; import java.util.Vector; //import javax.swing.JPanel; @@ -110,7 +110,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements private int actionOption = ACTION_OPTION_SELECT; - private ColumnSelection oldColumnSelection; + private HiddenColumns oldHiddenColumns; public AnnotationColumnChooser() { @@ -140,9 +140,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements { return; } - setOldColumnSelection(av.getColumnSelection()); + setOldHiddenColumns(av.getAlignment().getHiddenColumns()); adjusting = true; - Vector list = new Vector(); + Vector list = new Vector<>(); int index = 1; for (int i = 0; i < anns.length; i++) { @@ -167,20 +167,18 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements } populateThresholdComboBox(threshold); - + AnnotationColumnChooser lastChooser = av + .getAnnotationColumnSelectionState(); // restore Object state from the previous session if one exists - if (av.getAnnotationColumnSelectionState() != null) + if (lastChooser != null) { - currentSearchPanel = av.getAnnotationColumnSelectionState() - .getCurrentSearchPanel(); - currentStructureFilterPanel = av.getAnnotationColumnSelectionState() + currentSearchPanel = lastChooser.getCurrentSearchPanel(); + currentStructureFilterPanel = lastChooser .getCurrentStructureFilterPanel(); - annotations.select(av.getAnnotationColumnSelectionState() - .getAnnotations().getSelectedIndex()); - threshold.select(av.getAnnotationColumnSelectionState() - .getThreshold().getSelectedIndex()); - actionOption = av.getAnnotationColumnSelectionState() - .getActionOption(); + annotations.select(lastChooser.getAnnotations().getSelectedIndex()); + threshold.select(lastChooser.getThreshold().getSelectedIndex()); + actionOption = lastChooser.getActionOption(); + percentThreshold.setState(lastChooser.percentThreshold.getState()); } try @@ -204,6 +202,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements thresholdValue.setEnabled(false); thresholdValue.setColumns(7); + thresholdValue.setCaretPosition(0); ok.addActionListener(this); cancel.addActionListener(this); @@ -219,6 +218,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements // thresholdPanel.setFont(JvSwingUtils.getLabelFont()); // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]")); + percentThreshold.setLabel("As percentage"); + percentThreshold.addItemListener(this); + actionPanel.setBackground(Color.white); // actionPanel.setFont(JvSwingUtils.getLabelFont()); @@ -242,6 +244,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements thresholdPanel.add(getThreshold()); thresholdPanel.add(slider); thresholdPanel.add(thresholdValue); + thresholdPanel.add(percentThreshold); actionPanel.add(ok); actionPanel.add(cancel); @@ -282,27 +285,27 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements @SuppressWarnings("unchecked") public void reset() { - if (this.getOldColumnSelection() != null) + if (this.getOldHiddenColumns() != null) { av.getColumnSelection().clear(); if (av.getAnnotationColumnSelectionState() != null) { - ColumnSelection oldSelection = av - .getAnnotationColumnSelectionState() - .getOldColumnSelection(); - if (oldSelection != null && oldSelection.getHiddenColumns() != null - && !oldSelection.getHiddenColumns().isEmpty()) + HiddenColumns oldHidden = av.getAnnotationColumnSelectionState() + .getOldHiddenColumns(); + if (oldHidden != null) { - for (Iterator itr = oldSelection.getHiddenColumns() - .iterator(); itr.hasNext();) + ArrayList regions = oldHidden.getHiddenColumnsCopy(); + for (int[] positions : regions) { - int positions[] = itr.next(); av.hideColumns(positions[0], positions[1]); } } - av.setColumnSelection(oldSelection); + // TODO not clear why we need to hide all the columns (above) if we are + // going to copy the hidden columns over wholesale anyway + av.getAlignment().setHiddenColumns(oldHidden); } + av.sendSelection(); ap.paintAlignment(true); } @@ -313,7 +316,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements { if (!adjusting) { - thresholdValue.setText((slider.getValue() / 1000f) + ""); + setThresholdValueText(); valueChanged(!sliderDragging); } } @@ -391,63 +394,66 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements } AnnotationFilterParameter filterParams = new AnnotationFilterParameter(); - setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations() - .getSelectedIndex()]); + setCurrentAnnotation(av.getAlignment() + .getAlignmentAnnotation()[getAnnotations().getSelectedIndex()]); - int selectedThresholdItem = getSelectedThresholdItem(getThreshold() - .getSelectedIndex()); + int selectedThresholdItem = getSelectedThresholdItem( + getThreshold().getSelectedIndex()); slider.setEnabled(true); thresholdValue.setEnabled(true); + percentThreshold.setEnabled(true); if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD) { slider.setEnabled(false); thresholdValue.setEnabled(false); thresholdValue.setText(""); + percentThreshold.setEnabled(false); // build filter params } else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD) { if (getCurrentAnnotation().threshold == null) { - getCurrentAnnotation() - .setThreshold( - new jalview.datamodel.GraphLine( - (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f, - "Threshold", Color.black)); + getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine( + (getCurrentAnnotation().graphMax + - getCurrentAnnotation().graphMin) / 2f, + "Threshold", Color.black)); } adjusting = true; - float range = getCurrentAnnotation().graphMax * 1000 - - getCurrentAnnotation().graphMin * 1000; + // float range = getCurrentAnnotation().graphMax * 1000 + // - getCurrentAnnotation().graphMin * 1000; slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000)); slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000)); - slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000)); - thresholdValue.setText(getCurrentAnnotation().threshold.value + ""); + slider.setValue( + (int) (getCurrentAnnotation().threshold.value * 1000)); + setThresholdValueText(); // slider.setMajorTickSpacing((int) (range / 10f)); slider.setEnabled(true); thresholdValue.setEnabled(true); + percentThreshold.setEnabled(true); adjusting = false; // build filter params - filterParams - .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); - if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH) + filterParams.setThresholdType( + AnnotationFilterParameter.ThresholdType.NO_THRESHOLD); + if (getCurrentAnnotation().isQuantitative()) { filterParams .setThresholdValue(getCurrentAnnotation().threshold.value); if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD) { - filterParams - .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD); + filterParams.setThresholdType( + AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD); } else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD) { - filterParams - .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD); + filterParams.setThresholdType( + AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD); } } } @@ -478,13 +484,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements filterParams.setRegexString(currentSearchPanel.searchBox.getText()); if (currentSearchPanel.displayName.getState()) { - filterParams - .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING); + filterParams.addRegexSearchField( + AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING); } if (currentSearchPanel.description.getState()) { - filterParams - .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION); + filterParams.addRegexSearchField( + AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION); } } else @@ -494,10 +500,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements } } + // show hidden columns here, before changing the column selection in + // filterAnnotations, because showing hidden columns has the side effect of + // adding them to the selection + av.showAllHiddenColumns(); av.getColumnSelection().filterAnnotations( getCurrentAnnotation().annotations, filterParams); - av.showAllHiddenColumns(); if (getActionOption() == ACTION_OPTION_HIDE) { av.hideSelectedColumns(); @@ -505,19 +514,20 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements filterParams = null; av.setAnnotationColumnSelectionState(this); + av.sendSelection(); ap.paintAlignment(true); } - public ColumnSelection getOldColumnSelection() + public HiddenColumns getOldHiddenColumns() { - return oldColumnSelection; + return oldHiddenColumns; } - public void setOldColumnSelection(ColumnSelection currentColumnSelection) + public void setOldHiddenColumns(HiddenColumns currentHiddenColumns) { - if (currentColumnSelection != null) + if (currentHiddenColumns != null) { - this.oldColumnSelection = new ColumnSelection(currentColumnSelection); + this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns); } } @@ -574,13 +584,21 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements { threshold_actionPerformed(null); } + else if (e.getSource() == percentThreshold) + { + if (!adjusting) + { + percentageValue_actionPerformed(); + } + + } } public void selectedAnnotationChanged() { String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW; if (av.getAlignment().getAlignmentAnnotation()[getAnnotations() - .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH) + .getSelectedIndex()].isQuantitative()) { currentView = AnnotationColumnChooser.GRAPH_VIEW; } @@ -619,7 +637,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements public void syncState() { - if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE) + if (aColChooser + .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE) { furtherAction.select("Hide"); } @@ -647,8 +666,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements } } - public class StructureFilterPanel extends TitledPanel implements - ItemListener + public class StructureFilterPanel extends TitledPanel + implements ItemListener { private AnnotationColumnChooser aColChooser; @@ -877,19 +896,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements @Override public void actionPerformed(ActionEvent evt) { - if (evt.getSource() == thresholdValue) - { - try - { - float f = new Float(thresholdValue.getText()).floatValue(); - slider.setValue((int) (f * 1000)); - adjustmentValueChanged(null); - } catch (NumberFormatException ex) - { - } - } - else if (evt.getSource() == ok) + if (evt.getSource() == ok) { ok_actionPerformed(null); }