Protein Family Alignment Annotation Tool svncode

moved to src/org/pfaat/gui/common/dialogs

Moved to src.org.pfaat.core.msa.io

Moved to src.org.pfaat.gui.msa.find

Moved to src.org.pfaat.gui.msa.find

comment out checkbox color and button background color that are used by win but not used by mac

1) Renamed methods in Sequence to the following for clarity and consistency: getAnnotationValueDisplayedAt1stComponent getAnnotationValueDisplayedAt2ndComponent getAnnotationValueDisplayedAt3rdComponent getAnnotationNameForAnnotationValueDisplayedAt1stComponent getAnnotationNameForAnnotationValueDisplayedAt2ndComponent getAnnotationNameForAnnotationValueDisplayedAt3rdComponent. 2) Made the following changes to EditSeqAnnDialog.java EditSeqNameDialog.java: A) Dialogs are sized and positioned relative to the owner/AlignmentFrame (works better than before but not perfect). B) Text is is helvetica 14 to be consistent with Annotations viewed from the tree. C) Radio buttons are leftmost as they were not visible when the annotation names or values were long. 3) Some refs to renamed class that were mentioned in the last 2 commits

renamed, see previous commit

Renamed from src/com/neogenesis/pfaat/SequenceAnnComponent.java src/com/neogenesis/pfaat/SequenceNameComponent.java src/com/neogenesis/pfaat/AlignmentAnnPanel.java for clarity and to reflect actual function

The following changes were made to Edit sequence/Node annotations dialog: 1) Center the dialog relative to the tree graphic. 2) Set the size of the dialog relative to the tree graphic. 3) The show checkboxes are now on the left as they were not visible when the annotation values were long. 4) Made the text size bigger for annotation names and values. 5) Made the textfield for annotation values longer/bigger. 6) Changed the background color of all components to the default look and feel. 6). Move the show checkbox for spec/duplication to be leftmost.

1) Now calculates more accurate relative accessibilies for modified residues. 2) Prints warning whenever the max possible residue accessibility is exceeded or not set for a modified residue.