X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationColumnSelection.java;fp=src%2Fjalview%2Fgui%2FAnnotationColumnSelection.java;h=0000000000000000000000000000000000000000;hb=ead72caff9aef9b7103dbb15907aeae777200832;hp=ee8f03ab08b6dbf9d633cebc1f0770653a037411;hpb=1f8022f2b026e9852c76f0803d92da016a1bde5e;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColumnSelection.java b/src/jalview/gui/AnnotationColumnSelection.java
deleted file mode 100644
index ee8f03a..0000000
--- a/src/jalview/gui/AnnotationColumnSelection.java
+++ /dev/null
@@ -1,660 +0,0 @@
-package jalview.gui;
-
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.GraphLine;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
-import javax.swing.JLayeredPane;
-import javax.swing.JPanel;
-import javax.swing.JSlider;
-import javax.swing.JTextField;
-import javax.swing.event.ChangeEvent;
-import javax.swing.event.ChangeListener;
-
-import net.miginfocom.swing.MigLayout;
-
-public class AnnotationColumnSelection extends JPanel
-{
-  JInternalFrame frame;
-
-  AlignViewport av;
-
-  AlignmentPanel ap;
-
-  ColourSchemeI oldcs;
-
-  Hashtable oldgroupColours;
-
-  private JComboBox annotations;
-
-  int[] annmap;
-
-  JPanel minColour = new JPanel();
-
-  JPanel maxColour = new JPanel();
-
-  JButton defColours = new JButton();
-
-  JButton ok = new JButton();
-
-  JButton cancel = new JButton();
-
-  JPanel jPanel1 = new JPanel();
-
-  JPanel jPanel2 = new JPanel();
-
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  private JComboBox threshold = new JComboBox();
-
-  JSlider slider = new JSlider();
-
-  JTextField thresholdValue = new JTextField(20);
-
-  JCheckBox currentColours = new JCheckBox();
-
-  JCheckBox thresholdIsMin = new JCheckBox();
-
-  JCheckBox seqAssociated = new JCheckBox();
-
-  private jalview.datamodel.AlignmentAnnotation currentAnnotation;
-
-  boolean adjusting = false;
-
-  /**
-   * enabled if the user is dragging the slider - try to keep updates to a
-   * minimun
-   */
-  boolean sliderDragging = false;
-
-  public AnnotationColumnSelection(AlignViewport av, final AlignmentPanel ap)
-  {
-
-    this.av = av;
-    this.ap = ap;
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Select By Annotation", 520, 215);
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      @Override
-      public void stateChanged(ChangeEvent evt)
-      {
-        if (!adjusting)
-        {
-          thresholdValue.setText((slider.getValue() / 1000f) + "");
-          valueChanged(!sliderDragging);
-        }
-      }
-    });
-    slider.addMouseListener(new MouseAdapter()
-    {
-      @Override
-      public void mousePressed(MouseEvent e)
-      {
-        sliderDragging = true;
-        super.mousePressed(e);
-      }
-
-      @Override
-      public void mouseDragged(MouseEvent e)
-      {
-        sliderDragging = true;
-        super.mouseDragged(e);
-      }
-
-      @Override
-      public void mouseReleased(MouseEvent evt)
-      {
-        if (sliderDragging)
-        {
-          sliderDragging = false;
-          valueChanged(true);
-        }
-        ap.paintAlignment(true);
-      }
-    });
-
-    if (av.getAlignment().getAlignmentAnnotation() == null)
-    {
-      return;
-    }
-
-    // Always get default shading from preferences.
-    setDefaultMinMax();
-
-    adjusting = true;
-
-    setAnnotations(new JComboBox(
-            getAnnotationItems(seqAssociated.isSelected())));
-
-    threshold.addItem(MessageManager
-            .getString("label.threshold_feature_no_thereshold"));
-    threshold.addItem(MessageManager
-            .getString("label.threshold_feature_above_thereshold"));
-    threshold.addItem(MessageManager
-            .getString("label.threshold_feature_below_thereshold"));
-
-    if (av.getCurrentAnnotationColumnSelectionState() != null)
-    {
-      annotations.setSelectedIndex(av
-              .getCurrentAnnotationColumnSelectionState().getAnnotations()
-              .getSelectedIndex());
-      threshold.setSelectedIndex(av
-              .getCurrentAnnotationColumnSelectionState().getThreshold()
-              .getSelectedIndex());
-      System.out.println("selected annotation : "
-              + av.getCurrentAnnotationColumnSelectionState()
-                      .getAnnotations().getSelectedIndex());
-      System.out.println("selected threshold : "
-              + av.getCurrentAnnotationColumnSelectionState()
-                      .getThreshold().getSelectedIndex());
-    }
-
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-    }
-
-    adjusting = false;
-
-    changeColumnSelection();
-    frame.invalidate();
-    frame.pack();
-
-  }
-
-  private Vector<String> getAnnotationItems(boolean isSeqAssociated)
-  {
-    Vector<String> list = new Vector<String>();
-    int index = 1;
-    int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
-    boolean enableSeqAss = false;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
-    {
-      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
-      {
-        if (isSeqAssociated)
-        {
-          continue;
-        }
-      }
-      else
-      {
-        enableSeqAss = true;
-      }
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-      {
-        anmap[list.size()] = i;
-        list.add(label);
-
-      }
-      else
-      {
-        if (!isSeqAssociated)
-        {
-          anmap[list.size()] = i;
-          list.add(label + "_" + (index++));
-        }
-      }
-    }
-    seqAssociated.setEnabled(enableSeqAss);
-    this.annmap = new int[list.size()];
-    System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
-    return list;
-  }
-
-  private void setDefaultMinMax()
-  {
-    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
-            Color.orange));
-    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
-            Color.red));
-  }
-
-  public AnnotationColumnSelection()
-  {
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  private void jbInit() throws Exception
-  {
-    ok.setOpaque(false);
-    ok.setText(MessageManager.getString("action.ok"));
-    ok.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setOpaque(false);
-    cancel.setText(MessageManager.getString("action.cancel"));
-    cancel.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-
-    getAnnotations().addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        annotations_actionPerformed(e);
-      }
-    });
-    getThreshold().addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        threshold_actionPerformed(e);
-      }
-    });
-    thresholdValue.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdValue_actionPerformed(e);
-      }
-    });
-    slider.setPaintLabels(false);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setEnabled(false);
-    slider.setOpaque(false);
-    slider.setPreferredSize(new Dimension(100, 32));
-    thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(7);
-    thresholdIsMin.setBackground(Color.white);
-    thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
-    thresholdIsMin.setText(MessageManager
-            .getString("label.threshold_minmax"));
-    thresholdIsMin.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent actionEvent)
-      {
-        thresholdIsMin_actionPerformed(actionEvent);
-      }
-    });
-    seqAssociated.setBackground(Color.white);
-    seqAssociated.setFont(JvSwingUtils.getLabelFont());
-    seqAssociated.setText(MessageManager
-            .getString("label.per_sequence_only"));
-    seqAssociated.addActionListener(new ActionListener()
-    {
-
-      @Override
-      public void actionPerformed(ActionEvent arg0)
-      {
-        seqAssociated_actionPerformed(arg0);
-      }
-    });
-
-    this.setLayout(borderLayout1);
-    jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
-    jPanel1.setBackground(Color.white);
-    jPanel2.setBackground(Color.white);
-
-    jPanel1.add(ok);
-    jPanel1.add(cancel);
-    jPanel2.add(getAnnotations(), "grow, wrap");
-    jPanel2.add(seqAssociated, "wrap");
-    jPanel2.add(getThreshold(), "grow, wrap");
-    jPanel2.add(thresholdIsMin, "wrap");
-    jPanel2.add(slider, "grow");
-    jPanel2.add(thresholdValue, "grow");
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-    this.add(jPanel2, java.awt.BorderLayout.CENTER);
-    this.validate();
-  }
-
-  protected void seqAssociated_actionPerformed(ActionEvent arg0)
-  {
-    adjusting = true;
-    String cursel = (String) getAnnotations().getSelectedItem();
-    boolean isvalid = false, isseqs = seqAssociated.isSelected();
-    this.getAnnotations().removeAllItems();
-    for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
-    {
-      if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
-      {
-        isvalid = true;
-        cursel = anitem;
-      }
-      this.getAnnotations().addItem(anitem);
-    }
-    adjusting = false;
-    if (isvalid)
-    {
-      this.getAnnotations().setSelectedItem(cursel);
-    }
-    else
-    {
-      if (getAnnotations().getItemCount() > 0)
-      {
-        getAnnotations().setSelectedIndex(0);
-      }
-    }
-  }
-
-
-  void changeColumnSelection()
-  {
-    // Check if combobox is still adjusting
-    if (adjusting)
-    {
-      return;
-    }
-
-    setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
-            .getSelectedIndex()]]);
-
-    int aboveThreshold = -1;
-    if (getThreshold().getSelectedIndex() == 1)
-    {
-      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
-    }
-    else if (getThreshold().getSelectedIndex() == 2)
-    {
-      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
-    }
-
-    slider.setEnabled(true);
-    thresholdValue.setEnabled(true);
-    thresholdIsMin.setEnabled(true);
-
-    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
-    {
-      slider.setEnabled(false);
-      thresholdValue.setEnabled(false);
-      thresholdValue.setText("");
-      thresholdIsMin.setEnabled(false);
-    }
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
-            && getCurrentAnnotation().threshold == null)
-    {
-      getCurrentAnnotation()
-              .setThreshold(new jalview.datamodel.GraphLine(
-                              (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
-                      "Threshold", Color.black));
-    }
-
-    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
-    {
-      adjusting = true;
-      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.setMajorTickSpacing((int) (range / 10f));
-      slider.setEnabled(true);
-      thresholdValue.setEnabled(true);
-      adjusting = false;
-    }
-
-    markColumnsContaining(getCurrentAnnotation(), aboveThreshold);
-    av.setCurrentAnnotationColumnSelectionState(this);
-    ap.alignmentChanged();
-    // ensure all associated views (overviews, structures, etc) are notified of
-    // updated colours.
-    ap.paintAlignment(true);
-  }
-
-  public boolean markColumnsContaining(
-          AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
-  {
-    try
-    {
-      if (currentAnnotation != null)
-      {
-        Annotation[] annotations = currentAnnotation.annotations;
-        ColumnSelection cs = av.getColumnSelection();
-        cs.clear();
-        if (thresholdComparisonType == AnnotationColourGradient.NO_THRESHOLD)
-        {
-          int count = 0;
-          do
-          {
-            if (annotations[count] != null)
-            {
-              if (currentAnnotation.label.equals("Secondary Structure")
-                      && annotations[count].secondaryStructure != ' ')
-              {
-                cs.addElement(count);
-              }
-              else if (currentAnnotation.label
-                      .equals("Iron Sulphur Contacts"))
-              {
-                cs.addElement(count);
-              }
-              else if (annotations[count].value != 0.0)
-              {
-                cs.addElement(count);
-              }
-
-            }
-            count++;
-          } while (count < annotations.length);
-        }
-        else
-        {
-          int count = 0;
-          do
-          {
-            if (annotations[count] != null)
-            {
-              if (thresholdComparisonType == AnnotationColourGradient.ABOVE_THRESHOLD)
-              {
-                if (annotations[count].value > currentAnnotation.threshold.value)
-                {
-                  cs.addElement(count);
-                }
-              }
-              else if (thresholdComparisonType == AnnotationColourGradient.BELOW_THRESHOLD)
-              {
-                if (annotations[count].value < currentAnnotation.threshold.value)
-                {
-                  cs.addElement(count);
-                }
-              }
-
-            }
-            count++;
-          } while (count < annotations.length);
-        }
-      }
-
-      return true;
-    } catch (Exception e)
-    {
-      e.printStackTrace();
-      return false;
-    }
-  }
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    changeColumnSelection();
-    try
-    {
-      frame.setClosed(true);
-    } catch (Exception ex)
-    {
-    }
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    reset();
-    // ensure all original colouring is propagated to listeners.
-    ap.paintAlignment(true);
-    try
-    {
-      frame.setClosed(true);
-    } catch (Exception ex)
-    {
-    }
-  }
-
-  void reset()
-  {
-    av.getColumnSelection().clear();
-  }
-
-  public void thresholdCheck_actionPerformed(ActionEvent e)
-  {
-    changeColumnSelection();
-  }
-
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-    changeColumnSelection();
-  }
-
-  public void threshold_actionPerformed(ActionEvent e)
-  {
-    changeColumnSelection();
-  }
-
-  public void thresholdValue_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      float f = Float.parseFloat(thresholdValue.getText());
-      slider.setValue((int) (f * 1000));
-      changeColumnSelection();
-    } catch (NumberFormatException ex)
-    {
-    }
-  }
-
-  public void valueChanged(boolean updateAllAnnotation)
-  {
-    getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
-    changeColumnSelection();
-    // propagateSeqAssociatedThreshold(updateAllAnnotation);
-    ap.paintAlignment(false);
-  }
-
-  private void propagateSeqAssociatedThreshold(boolean allAnnotation)
-  {
-    if (getCurrentAnnotation().sequenceRef == null
-            || getCurrentAnnotation().threshold == null)
-    {
-      return;
-    }
-
-
-    float thr = getCurrentAnnotation().threshold.value;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
-    {
-      AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
-      if (aa.label.equals(getCurrentAnnotation().label)
-              && (getCurrentAnnotation().getCalcId() == null ? aa
-                      .getCalcId() == null : getCurrentAnnotation()
-                      .getCalcId()
-                              .equals(aa.getCalcId())))
-      {
-        if (aa.threshold == null)
-        {
-          aa.threshold = new GraphLine(getCurrentAnnotation().threshold);
-        }
-        else
-        {
-          aa.threshold.value = thr;
-        }
-      }
-    }
-  }
-
-  public void currentColours_actionPerformed(ActionEvent e)
-  {
-    if (currentColours.isSelected())
-    {
-      reset();
-    }
-
-    maxColour.setEnabled(!currentColours.isSelected());
-    minColour.setEnabled(!currentColours.isSelected());
-
-    changeColumnSelection();
-  }
-
-  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
-  {
-    changeColumnSelection();
-  }
-
-  public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
-  {
-    return currentAnnotation;
-  }
-
-  public void setCurrentAnnotation(
-          jalview.datamodel.AlignmentAnnotation currentAnnotation)
-  {
-    this.currentAnnotation = currentAnnotation;
-  }
-
-  public JComboBox getThreshold()
-  {
-    return threshold;
-  }
-
-  public void setThreshold(JComboBox threshold)
-  {
-    this.threshold = threshold;
-  }
-
-  public JComboBox getAnnotations()
-  {
-    return annotations;
-  }
-
-  public void setAnnotations(JComboBox annotations)
-  {
-    this.annotations = annotations;
-  }
-
-}