From: gmungoc Date: Fri, 30 Sep 2016 12:51:59 +0000 (+0100) Subject: JAL-2236 code restored (and some compiler warnings addressed) X-Git-Tag: Release_2_10_0~22 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a49b953d151391cd9526a7655997c6409f20306c;p=jalview.git JAL-2236 code restored (and some compiler warnings addressed) --- diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index 93c9a6b..39cde03 100644 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -210,7 +210,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent e) { - ok_actionPerformed(e); + ok_actionPerformed(); } }); cancel.setOpaque(false); @@ -220,7 +220,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent e) { - cancel_actionPerformed(e); + cancel_actionPerformed(); } }); defColours.setOpaque(false); @@ -233,7 +233,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent arg0) { - resetColours_actionPerformed(arg0); + resetColours_actionPerformed(); } }); @@ -242,7 +242,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent e) { - annotations_actionPerformed(e); + annotations_actionPerformed(); } }); getThreshold().addActionListener(new ActionListener() @@ -250,7 +250,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent e) { - threshold_actionPerformed(e); + threshold_actionPerformed(); } }); thresholdValue.addActionListener(new ActionListener() @@ -258,7 +258,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent e) { - thresholdValue_actionPerformed(e); + thresholdValue_actionPerformed(); } }); slider.setPaintLabels(false); @@ -278,7 +278,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent e) { - currentColours_actionPerformed(e); + currentColours_actionPerformed(); } }); thresholdIsMin.setBackground(Color.white); @@ -290,7 +290,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent actionEvent) { - thresholdIsMin_actionPerformed(actionEvent); + thresholdIsMin_actionPerformed(); } }); seqAssociated.setBackground(Color.white); @@ -303,7 +303,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter @Override public void actionPerformed(ActionEvent arg0) { - seqAssociated_actionPerformed(arg0, annotations, seqAssociated); + seqAssociated_actionPerformed(annotations); } }); @@ -332,7 +332,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter this.validate(); } - protected void resetColours_actionPerformed(ActionEvent arg0) + protected void resetColours_actionPerformed() { setDefaultMinMax(); updateView(); @@ -372,6 +372,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter updateView(); } + @Override public void reset() { av.setGlobalColourScheme(oldcs); @@ -385,6 +386,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter } } + @Override public void valueChanged(boolean updateAllAnnotation) { if (slider.isEnabled()) @@ -411,7 +413,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter this.threshold = threshold; } - public void currentColours_actionPerformed(ActionEvent e) + public void currentColours_actionPerformed() { if (currentColours.isSelected()) { diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java index c0d7084..1290d70 100644 --- a/src/jalview/gui/AnnotationColumnChooser.java +++ b/src/jalview/gui/AnnotationColumnChooser.java @@ -178,7 +178,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements @Override public void actionPerformed(ActionEvent e) { - ok_actionPerformed(e); + ok_actionPerformed(); } }); @@ -189,7 +189,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements @Override public void actionPerformed(ActionEvent e) { - cancel_actionPerformed(e); + cancel_actionPerformed(); } }); @@ -201,7 +201,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements @Override public void actionPerformed(ActionEvent e) { - threshold_actionPerformed(e); + threshold_actionPerformed(); } }); @@ -212,7 +212,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements @Override public void actionPerformed(ActionEvent e) { - thresholdValue_actionPerformed(e); + thresholdValue_actionPerformed(); } }); @@ -288,14 +288,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements String defaultTtip = MessageManager .getString("info.change_threshold_mode_to_enable"); - String threshold = getThreshold().getSelectedItem().toString(); - if (threshold.equalsIgnoreCase("No Threshold")) + String thresh = getThreshold().getSelectedItem().toString(); + if (thresh.equalsIgnoreCase("No Threshold")) { thresholdValue.setToolTipText(defaultTtip); slider.setToolTipText(defaultTtip); } } + @Override public void reset() { if (this.getOldColumnSelection() != null) @@ -324,6 +325,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements } + @Override public void valueChanged(boolean updateAllAnnotation) { if (slider.isEnabled()) diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java index 8335042..37f1e55 100644 --- a/src/jalview/gui/AnnotationRowFilter.java +++ b/src/jalview/gui/AnnotationRowFilter.java @@ -26,7 +26,6 @@ import jalview.datamodel.SequenceGroup; import jalview.schemes.AnnotationColourGradient; import jalview.util.MessageManager; -import java.awt.event.ActionEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.util.Vector; @@ -52,7 +51,7 @@ public abstract class AnnotationRowFilter extends JPanel protected boolean enableSeqAss = false; - private jalview.datamodel.AlignmentAnnotation currentAnnotation; + private AlignmentAnnotation currentAnnotation; protected boolean adjusting = false; @@ -162,7 +161,8 @@ public abstract class AnnotationRowFilter extends JPanel } String label = av.getAlignment().getAlignmentAnnotation()[i].label; // add associated sequence ID if available - if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null) + if (!isSeqAssociated + && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null) { label = label + "_" @@ -208,7 +208,7 @@ public abstract class AnnotationRowFilter extends JPanel seqAssociated.setEnabled(enableSeqAss); } - public void ok_actionPerformed(ActionEvent e) + public void ok_actionPerformed() { try { @@ -218,7 +218,7 @@ public abstract class AnnotationRowFilter extends JPanel } } - public void cancel_actionPerformed(ActionEvent e) + public void cancel_actionPerformed() { reset(); ap.paintAlignment(true); @@ -230,22 +230,22 @@ public abstract class AnnotationRowFilter extends JPanel } } - public void thresholdCheck_actionPerformed(ActionEvent e) + public void thresholdCheck_actionPerformed() { updateView(); } - public void annotations_actionPerformed(ActionEvent e) + public void annotations_actionPerformed() { updateView(); } - public void threshold_actionPerformed(ActionEvent e) + public void threshold_actionPerformed() { updateView(); } - public void thresholdValue_actionPerformed(ActionEvent e) + public void thresholdValue_actionPerformed() { try { @@ -257,7 +257,7 @@ public abstract class AnnotationRowFilter extends JPanel } } - public void thresholdIsMin_actionPerformed(ActionEvent actionEvent) + public void thresholdIsMin_actionPerformed() { updateView(); } @@ -272,8 +272,7 @@ public abstract class AnnotationRowFilter extends JPanel .getString("label.threshold_feature_below_threshold")); } - protected void seqAssociated_actionPerformed(ActionEvent arg0, - JComboBox annotations, JCheckBox seqAssociated) + protected void seqAssociated_actionPerformed(JComboBox annotations) { adjusting = true; String cursel = (String) annotations.getSelectedItem(); @@ -331,25 +330,25 @@ public abstract class AnnotationRowFilter extends JPanel } protected boolean colorAlignmContaining( - AlignmentAnnotation currentAnnotation, int selectedThresholdItem) + AlignmentAnnotation currentAnn, int selectedThresholdOption) { AnnotationColourGradient acg = null; if (currentColours.isSelected()) { - acg = new AnnotationColourGradient(currentAnnotation, - av.getGlobalColourScheme(), selectedThresholdItem); + acg = new AnnotationColourGradient(currentAnn, + av.getGlobalColourScheme(), selectedThresholdOption); } else { - acg = new AnnotationColourGradient(currentAnnotation, + acg = new AnnotationColourGradient(currentAnn, minColour.getBackground(), maxColour.getBackground(), - selectedThresholdItem); + selectedThresholdOption); } acg.setSeqAssociated(seqAssociated.isSelected()); - if (currentAnnotation.graphMin == 0f - && currentAnnotation.graphMax == 0f) + if (currentAnn.graphMin == 0f + && currentAnn.graphMax == 0f) { acg.setPredefinedColours(true); } @@ -370,17 +369,17 @@ public abstract class AnnotationRowFilter extends JPanel if (currentColours.isSelected()) { - sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs, - selectedThresholdItem); + sg.cs = new AnnotationColourGradient(currentAnn, sg.cs, + selectedThresholdOption); ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated .isSelected()); } else { - sg.cs = new AnnotationColourGradient(currentAnnotation, + sg.cs = new AnnotationColourGradient(currentAnn, minColour.getBackground(), maxColour.getBackground(), - selectedThresholdItem); + selectedThresholdOption); ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated .isSelected()); }