*/
package jalview.gui;
-import jalview.analysis.TreeBuilder;
-import jalview.analysis.scoremodels.ScoreModels;
-import jalview.analysis.scoremodels.SimilarityParams;
-import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.SimilarityParamsI;
-import jalview.datamodel.SequenceGroup;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+
/**
* A dialog where a user can choose and action Tree or PCA calculation options
*/
final ComboBoxTooltipRenderer renderer = new ComboBoxTooltipRenderer();
- List<String> tips = new ArrayList<String>();
+ List<String> tips = new ArrayList<>();
+
+ /*
+ * the most recently opened PCA results panel
+ */
+ private PCAPanel pcaPanel;
/**
* Constructor
{
setLayout(new BorderLayout());
frame = new JInternalFrame();
+ frame.setFrameIcon(null);
frame.setContentPane(this);
this.setBackground(Color.white);
frame.addFocusListener(new FocusListener()
pca = new JRadioButton(
MessageManager.getString("label.principal_component_analysis"));
pca.setOpaque(false);
+
neighbourJoining = new JRadioButton(
MessageManager.getString("label.tree_calc_nj"));
neighbourJoining.setSelected(true);
+ neighbourJoining.setOpaque(false);
+
averageDistance = new JRadioButton(
MessageManager.getString("label.tree_calc_av"));
- neighbourJoining.setOpaque(false);
+ averageDistance.setOpaque(false);
JPanel calcChoicePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
calcChoicePanel.setOpaque(false);
JPanel treePanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
treePanel.setOpaque(false);
- treePanel.setBorder(BorderFactory.createTitledBorder(MessageManager
- .getString("label.tree")));
+ JvSwingUtils.createTitledBorder(treePanel,
+ MessageManager.getString("label.tree"), true);
// then copy the inset dimensions for the border-less PCA panel
JPanel pcaBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT));
Insets b = treePanel.getBorder().getBorderInsets(treePanel);
- pcaBorderless.setBorder(BorderFactory.createEmptyBorder(2, b.left, 2,
- b.right));
+ pcaBorderless.setBorder(
+ BorderFactory.createEmptyBorder(2, b.left, 2, b.right));
pcaBorderless.setOpaque(false);
pcaBorderless.add(pca, FlowLayout.LEFT);
calcTypes.add(pca);
calcTypes.add(neighbourJoining);
calcTypes.add(averageDistance);
-
+
ActionListener calcChanged = new ActionListener()
{
@Override
setMinimumSize(new Dimension(325, height - 10));
String title = MessageManager.getString("label.choose_calculation");
- if (af.getViewport().viewName != null)
+ if (af.getViewport().getViewName() != null)
{
- title = title + " (" + af.getViewport().viewName + ")";
+ title = title + " (" + af.getViewport().getViewName() + ")";
}
Desktop.addInternalFrame(frame, title, width, height, false);
};
});
+ validateCalcTypes();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
}
*/
private boolean checkEnabled(JRadioButton calc, int size, int minsize)
{
- String ttip = MessageManager.formatMessage(
- "label.you_need_at_least_n_sequences", minsize);
+ String ttip = MessageManager
+ .formatMessage("label.you_need_at_least_n_sequences", minsize);
calc.setEnabled(size >= minsize);
if (!calc.isEnabled())
*/
protected JComboBox<String> buildModelOptionsList()
{
- final JComboBox<String> scoreModelsCombo = new JComboBox<String>();
+ final JComboBox<String> scoreModelsCombo = new JComboBox<>();
scoreModelsCombo.setRenderer(renderer);
/*
@Override
public void mouseEntered(MouseEvent e)
{
- scoreModelsCombo.setToolTipText(tips.get(scoreModelsCombo.getSelectedIndex()));
+ scoreModelsCombo.setToolTipText(
+ tips.get(scoreModelsCombo.getSelectedIndex()));
}
@Override
{
Object curSel = comboBox.getSelectedItem();
toolTips.clear();
- DefaultComboBoxModel<String> model = new DefaultComboBoxModel<String>();
+ DefaultComboBoxModel<String> model = new DefaultComboBoxModel<>();
+
+ /*
+ * select the score models applicable to the alignment type
+ */
+ boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
+ List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
+ pca.isSelected());
/*
* now we can actually add entries to the combobox,
* remembering their descriptions for tooltips
*/
- ScoreModels scoreModels = ScoreModels.getInstance();
boolean selectedIsPresent = false;
- for (ScoreModelI sm : scoreModels.getModels())
+ for (ScoreModelI sm : models)
{
- boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
- if (sm.isDNA() && nucleotide || sm.isProtein() && !nucleotide)
+ if (curSel != null && sm.getName().equals(curSel))
+ {
+ selectedIsPresent = true;
+ curSel = sm.getName();
+ }
+ model.addElement(sm.getName());
+
+ /*
+ * tooltip is description if provided, else text lookup with
+ * fallback on the model name
+ */
+ String tooltip = sm.getDescription();
+ if (tooltip == null)
{
- if (curSel != null && sm.getName().equals(curSel))
- {
- selectedIsPresent = true;
- curSel = sm.getName();
- }
- model.addElement(sm.getName());
-
- /*
- * tooltip is description if provided, else text lookup with
- * fallback on the model name
- */
- String tooltip = sm.getDescription();
- if (tooltip == null)
- {
- tooltip = MessageManager.getStringOrReturn("label.score_model_",
- sm.getName());
- }
- toolTips.add(tooltip);
+ tooltip = MessageManager.getStringOrReturn("label.score_model_",
+ sm.getName());
}
+ toolTips.add(tooltip);
}
+
if (selectedIsPresent)
{
model.setSelectedItem(curSel);
}
/**
+ * Builds a list of score models which are applicable for the alignment and
+ * calculation type (peptide or generic models for protein, nucleotide or
+ * generic models for nucleotide).
+ * <p>
+ * As a special case, includes BLOSUM62 as an extra option for nucleotide PCA.
+ * This is for backwards compatibility with Jalview prior to 2.8 when BLOSUM62
+ * was the only score matrix supported. This is included if property
+ * BLOSUM62_PCA_FOR_NUCLEOTIDE is set to true in the Jalview properties file.
+ *
+ * @param nucleotide
+ * @param forPca
+ * @return
+ */
+ protected static List<ScoreModelI> getApplicableScoreModels(
+ boolean nucleotide, boolean forPca)
+ {
+ List<ScoreModelI> filtered = new ArrayList<>();
+
+ ScoreModels scoreModels = ScoreModels.getInstance();
+ for (ScoreModelI sm : scoreModels.getModels())
+ {
+ if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA())
+ {
+ filtered.add(sm);
+ }
+ }
+
+ /*
+ * special case: add BLOSUM62 as last option for nucleotide PCA,
+ * for backwards compatibility with Jalview < 2.8 (JAL-2962)
+ */
+ if (nucleotide && forPca
+ && Cache.getDefault("BLOSUM62_PCA_FOR_NUCLEOTIDE", false))
+ {
+ filtered.add(scoreModels.getBlosum62());
+ }
+
+ return filtered;
+ }
+
+ /**
* Open and calculate the selected tree or PCA on 'OK'
*/
protected void calculate_actionPerformed()
SequenceGroup sg = viewport.getSelectionGroup();
if (sg != null && sg.getSize() < MIN_TREE_SELECTION)
{
- JvOptionPane
- .showMessageDialog(
- Desktop.desktop,
- MessageManager
- .formatMessage("label.you_need_at_least_n_sequences",
+ JvOptionPane.showMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.you_need_at_least_n_sequences",
MIN_TREE_SELECTION),
- MessageManager
- .getString("label.not_enough_sequences"),
- JvOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.not_enough_sequences"),
+ JvOptionPane.WARNING_MESSAGE);
return;
}
- String treeType = neighbourJoining.isSelected() ? TreeBuilder.NEIGHBOUR_JOINING
+ String treeType = neighbourJoining.isSelected()
+ ? TreeBuilder.NEIGHBOUR_JOINING
: TreeBuilder.AVERAGE_DISTANCE;
af.newTreePanel(treeType, modelName, params);
}
* this check in in case this method gets exposed programmatically in future
*/
if (((viewport.getSelectionGroup() != null)
- && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION) && (viewport
- .getSelectionGroup().getSize() > 0))
+ && (viewport.getSelectionGroup().getSize() < MIN_PCA_SELECTION)
+ && (viewport.getSelectionGroup().getSize() > 0))
|| (viewport.getAlignment().getHeight() < MIN_PCA_SELECTION))
{
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.you_need_at_least_n_sequences",
- MIN_PCA_SELECTION), MessageManager
- .getString("label.sequence_selection_insufficient"),
+ JvOptionPane.showInternalMessageDialog(this,
+ MessageManager.formatMessage(
+ "label.you_need_at_least_n_sequences",
+ MIN_PCA_SELECTION),
+ MessageManager
+ .getString("label.sequence_selection_insufficient"),
JvOptionPane.WARNING_MESSAGE);
return;
}
- new PCAPanel(af.alignPanel, modelName, params);
+
+ /*
+ * construct the panel and kick off its calculation thread
+ */
+ pcaPanel = new PCAPanel(af.alignPanel, modelName, params);
+ new Thread(pcaPanel).start();
+
}
/**
*/
boolean matchGap = doPCA ? false : treeMatchGaps;
- return new SimilarityParams(includeGapGap, matchGap, includeGapResidue, matchOnShortestLength);
+ return new SimilarityParams(includeGapGap, matchGap, includeGapResidue,
+ matchOnShortestLength);
}
/**
{
}
}
+
+ public PCAPanel getPcaPanel()
+ {
+ return pcaPanel;
+ }
}
git://source.jalview.org / jalview.git / blobdiff