Show all bases with IGV

Today someone asked me if I can make a revised version of snpview to support "Show all bases".

Manual operations shows that it required to right-click the alignment and select "Show all bases" from popped menu.

http://www.broadinstitute.org/igv/PortCommands

The supported socket commands for IGV does not include this operation. (In fact it only supports a very few commands)

Since IGV is open resource I decide to check out the source code to see if I can change the code then build a "Show all bases by default" IGV.

1. Find which source file is responsible for this option

>grep -r -n "Show all bases" IGVDistribution_2.1.14/src/

src/org/broad/igv/sam/AlignmentTrack.java:1533:            final JMenuItem item = new JCheckBoxMenuItem("Show all bases");

2. OK let us check this file "src/org/broad/igv/sam/AlignmentTrack.java"

vim +1533 src/org/broad/igv/sam/AlignmentTrack.java


The context shows:
*************************************************************
public void addShowAllBasesMenuItem() {
            // Change track height by attribute
            final JMenuItem item = new JCheckBoxMenuItem("Show all bases");

            if (renderOptions.colorOption == ColorOption.BISULFITE || renderOptions.colorOption == ColorOption.NOMESEQ) {
                //    item.setEnabled(false);
            } else {
                item.setSelected(renderOptions.showAllBases);
            }
            item.addActionListener(new ActionListener() {
                public void actionPerformed(ActionEvent aEvt) {
                    renderOptions.showAllBases = item.isSelected();
                    refresh();
                }
            });
            add(item);
        }
*************************************************************


It looks like "renderOptions.showAllBases" controls the switch on/off.

3. Check the  "renderOptions.showAllBases"
grep -r -n "renderOptions.showAllBases" IGVDistribution_2.1.14/src/

src/org/broad/igv/sam/AlignmentTrack.java:1538:                item.setSelected(renderOptions.showAllBases);
src/org/broad/igv/sam/AlignmentTrack.java:1542:                    renderOptions.showAllBases = item.isSelected();
src/org/broad/igv/sam/AlignmentRenderer.java:556:                if (renderOptions.showMismatches || renderOptions.showAllBases) {
src/org/broad/igv/sam/AlignmentRenderer.java:635:        boolean showAllBases = renderOptions.showAllBases &&



Notice the last line defines a boolean variable "boolean showAllBases ..."

Is this what I am looking for?

4. Further investigation
vim +635 src/org/broad/igv/sam/AlignmentRenderer.java


The context shows:
*************************************************************
// Disable showAllBases in bisulfite mode
        boolean showAllBases = renderOptions.showAllBases &&
                !(colorOption == ColorOption.BISULFITE || colorOption == ColorOption.NOMESEQ);

*************************************************************

Now it is quite clear: "showAllBases" controls the on/off of "Show all bases".

5. Now let us make a dirty patch

*************************************************************
// Disable showAllBases in bisulfite mode
//        boolean showAllBases = renderOptions.showAllBases &&
//                !(colorOption == ColorOption.BISULFITE || colorOption == ColorOption.NOMESEQ);

boolean showAllBases = true;

*************************************************************

We just set "true" to it for always "on"! Like I said, it is dirty because it completely ignore all options there.
It may have potential problem, but at now, let us make a test.

6. Go back to the source and build

>ant


We will got a new "igv.jar". rename it as "igv_showallbases.jar" to discriminate the original one.
>mv igv.jar igv_showallbases.jar

7. Test!

java -jar igv_showallbases.jar

It works! Now by default all bases in alignment are showed. 

The user is happy because he got what he wants!