*/
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.bin.Cache;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
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.AlignmentUtils;
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.AlignmentAnnotation;
import jalview.datamodel.SequenceGroup;
import jalview.util.MessageManager;
private static final int MIN_TREE_SELECTION = 3;
private static final int MIN_PCA_SELECTION = 4;
+
+ private String secondaryStructureModelName;
+
+ private void getSecondaryStructureModelName() {
+
+ ScoreModels scoreModels = ScoreModels.getInstance();
+ for (ScoreModelI sm : scoreModels.getModels())
+ {
+ if (sm.isSecondaryStructure())
+ {
+ secondaryStructureModelName = sm.getName();
+ }
+ }
+
+ }
+
+ private static final int MIN_PASIMAP_SELECTION = 8;
AlignFrame af;
JRadioButton pca;
+ JRadioButton pasimap;
+
JRadioButton neighbourJoining;
JRadioButton averageDistance;
JComboBox<String> modelNames;
+
+ JComboBox<String> ssSourceDropdown;
JButton calculate;
*/
private PCAPanel pcaPanel;
+ private PaSiMapPanel pasimapPanel;
+
/**
* Constructor
*
this.af = alignFrame;
init();
af.alignPanel.setCalculationDialog(this);
+
}
/**
*/
void init()
{
+ getSecondaryStructureModelName();
setLayout(new BorderLayout());
frame = new JInternalFrame();
frame.setFrameIcon(null);
MessageManager.getString("label.principal_component_analysis"));
pca.setOpaque(false);
+ pasimap = new JRadioButton( // create the JRadioButton for pasimap with label.pasimap as its text
+ MessageManager.getString("label.pasimap"));
+ pasimap.setOpaque(false);
+
neighbourJoining = new JRadioButton(
MessageManager.getString("label.tree_calc_nj"));
neighbourJoining.setSelected(true);
pcaBorderless.add(pca, FlowLayout.LEFT);
calcChoicePanel.add(pcaBorderless, FlowLayout.LEFT);
+ // create pasimap panel
+ JPanel pasimapBorderless = new JPanel(new FlowLayout(FlowLayout.LEFT)); // create new JPanel (button) for pasimap
+ pasimapBorderless.setBorder(
+ BorderFactory.createEmptyBorder(2, b.left, 2, b.right)); // set border (margin) for button (same as treePanel and pca)
+ pasimapBorderless.setOpaque(false); // false -> stops every pixel inside border from being painted
+ pasimapBorderless.add(pasimap, FlowLayout.LEFT); // add pasimap button to the JPanel
+ calcChoicePanel.add(pasimapBorderless, FlowLayout.LEFT); // add button with border and everything to the overall ChoicePanel
+
treePanel.add(neighbourJoining);
treePanel.add(averageDistance);
ButtonGroup calcTypes = new ButtonGroup();
calcTypes.add(pca);
+ calcTypes.add(pasimap);
calcTypes.add(neighbourJoining);
calcTypes.add(averageDistance);
}
};
pca.addActionListener(calcChanged);
+ pasimap.addActionListener(calcChanged); // add the calcChanged ActionListener to pasimap --> <++> idk
neighbourJoining.addActionListener(calcChanged);
averageDistance.addActionListener(calcChanged);
+
+
+ //to do
+ ssSourceDropdown = buildSSSourcesOptionsList();
+ ssSourceDropdown.setVisible(false); // Initially hide the dropdown
/*
* score models drop-down - with added tooltips!
*/
modelNames = buildModelOptionsList();
+
+ // Step 3: Show or Hide Dropdown Based on Selection
+ modelNames.addActionListener(new ActionListener() {
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ String selectedModel = modelNames.getSelectedItem().toString();
+
+ if (selectedModel.equals(secondaryStructureModelName)) {
+ ssSourceDropdown.setVisible(true);
+ } else {
+ ssSourceDropdown.setVisible(false);
+ }
+ }
+ });
+
JPanel scoreModelPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
scoreModelPanel.setOpaque(false);
scoreModelPanel.add(modelNames);
-
+ scoreModelPanel.add(ssSourceDropdown);
+
/*
* score model parameters
*/
paramsPanel.add(matchGaps);
paramsPanel.add(includeGappedColumns);
paramsPanel.add(shorterSequence);
-
+
/*
* OK / Cancel buttons
*/
}
this.add(actionPanel, BorderLayout.SOUTH);
- int width = 350;
+ int width = 365;
int height = includeParams ? 420 : 240;
setMinimumSize(new Dimension(325, height - 10));
* return value of true means enabled and selected
*/
boolean checkPca = checkEnabled(pca, size, MIN_PCA_SELECTION);
+ boolean checkPasimap = checkEnabled(pasimap, size, MIN_PASIMAP_SELECTION); // check if pasimap is enabled and min_size is fulfilled
boolean checkNeighbourJoining = checkEnabled(neighbourJoining, size,
MIN_TREE_SELECTION);
boolean checkAverageDistance = checkEnabled(averageDistance, size,
MIN_TREE_SELECTION);
- if (checkPca || checkNeighbourJoining || checkAverageDistance)
+ if (checkPca || checkPasimap || checkNeighbourJoining || checkAverageDistance)
{
calculate.setToolTipText(null);
calculate.setEnabled(true);
return scoreModelsCombo;
}
+
+
+ private JComboBox<String> buildSSSourcesOptionsList()
+ {
+ final JComboBox<String> comboBox = new JComboBox<>();
+ Object curSel = comboBox.getSelectedItem();
+ DefaultComboBoxModel<String> sourcesModel = new DefaultComboBoxModel<>();
+
+ List<String> ssSources = getApplicableSecondaryStructureSources();
+
+ boolean selectedIsPresent = false;
+ for (String source : ssSources)
+ {
+ if (curSel != null && source.equals(curSel))
+ {
+ selectedIsPresent = true;
+ curSel = source;
+ }
+ sourcesModel.addElement(source);
+
+ }
+ if (selectedIsPresent)
+ {
+ sourcesModel.setSelectedItem(curSel);
+ }
+ comboBox.setModel(sourcesModel);
+
+ return comboBox;
+ }
+
+
private void updateScoreModels(JComboBox<String> comboBox,
List<String> toolTips)
{
* select the score models applicable to the alignment type
*/
boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
- List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
- pca.isSelected());
+ AlignmentAnnotation[] alignmentAnnotations = af.getViewport().getAlignment().getAlignmentAnnotation();
+
+ boolean ssPresent = AlignmentUtils.isSecondaryStructurePresent(alignmentAnnotations);
+
+ List<ScoreModelI> models = getApplicableScoreModels(nucleotide, pca.isSelected(),
+ ssPresent);
/*
* now we can actually add entries to the combobox,
}
// finally, update the model
comboBox.setModel(model);
+
}
/**
* @return
*/
protected static List<ScoreModelI> getApplicableScoreModels(
- boolean nucleotide, boolean forPca)
+ boolean nucleotide, boolean forPca, boolean ssPresent)
{
List<ScoreModelI> filtered = new ArrayList<>();
ScoreModels scoreModels = ScoreModels.getInstance();
for (ScoreModelI sm : scoreModels.getModels())
{
- if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA())
+ if (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA()
+ || ssPresent && sm.isSecondaryStructure())
{
filtered.add(sm);
}
{
filtered.add(scoreModels.getBlosum62());
}
-
+
return filtered;
}
+
+ protected List<String> getApplicableSecondaryStructureSources()
+ {
+ AlignmentAnnotation[] annotations = af.getViewport().getAlignment().getAlignmentAnnotation();
+
+ List<String> ssSources = AlignmentUtils.getSecondaryStructureSources(annotations);
+ //List<String> ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
+
+
+ return ssSources;
+ }
+
/**
* Open and calculate the selected tree or PCA on 'OK'
*/
protected void calculate_actionPerformed()
{
boolean doPCA = pca.isSelected();
+ boolean doPaSiMap = pasimap.isSelected();
String modelName = modelNames.getSelectedItem().toString();
- SimilarityParamsI params = getSimilarityParameters(doPCA);
+ String ssSource = "";
+ Object selectedItem = ssSourceDropdown.getSelectedItem();
+ if (selectedItem != null) {
+ ssSource = selectedItem.toString();
+ }
+ SimilarityParams params = getSimilarityParameters(doPCA);
+ if(ssSource.length()>0)
+ {
+ params.setSecondaryStructureSource(ssSource);
+ }
- if (doPCA)
+ if (doPCA && !doPaSiMap)
{
openPcaPanel(modelName, params);
}
+ else if (doPaSiMap && !doPCA)
+ {
+ openPasimapPanel(modelName, params);
+ }
else
{
openTreePanel(modelName, params);
}
- // closeFrame();
+ closeFrame();
}
/**
}
/**
+ * Open a new PaSiMap panel on the desktop
+ *
+ * @param modelName
+ * @param params
+ */
+ protected void openPasimapPanel(String modelName, SimilarityParamsI params)
+ {
+ AlignViewport viewport = af.getViewport();
+
+ /*
+ * gui validation shouldn't allow insufficient sequences here, but leave
+ * this check in in case this method gets exposed programmatically in future
+ */
+ if (((viewport.getSelectionGroup() != null)
+ && (viewport.getSelectionGroup().getSize() < MIN_PASIMAP_SELECTION)
+ && (viewport.getSelectionGroup().getSize() > 0))
+ || (viewport.getAlignment().getHeight() < MIN_PASIMAP_SELECTION))
+ {
+ JvOptionPane.showInternalMessageDialog(this,
+ MessageManager.formatMessage(
+ "label.you_need_at_least_n_sequences",
+ MIN_PASIMAP_SELECTION),
+ MessageManager
+ .getString("label.sequence_selection_insufficient"),
+ JvOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ /*
+ * construct the panel and kick off its calculation thread
+ */
+ pasimapPanel = new PaSiMapPanel(af.alignPanel, modelName, params);
+ new Thread(pasimapPanel).start();
+
+ }
+
+ /**
*
*/
protected void closeFrame()
* @param doPCA
* @return
*/
- protected SimilarityParamsI getSimilarityParameters(boolean doPCA)
+ protected SimilarityParams getSimilarityParameters(boolean doPCA)
{
// commented out: parameter choices read from gui widgets
// SimilarityParamsI params = new SimilarityParams(
git://source.jalview.org / jalview.git / blobdiff