#27 consesus for big seqs(follow up)

[dcaffrey]

The consensus and conservation score are displayed incorrectly when the sequence is greater than 3640. e.g. a sequence of 3641 cause the consensus for column one to be displayed below col 2. A seq of size-3642 causes the consensus for column one to be displayed below col 2.

[dcaffrey]

Logged In: YES
user_id=1040751
Originator: YES

It looks like this is due to a layout problem as adding the code below to consensusComponent.java indicates that the entire component is shifted to the right as a red line at x=0 is shifted right.
//////////////////////////////////////////
//Draw a red line at the beginning of component
//this is useful for debugging incorrect placement
//of the component
//g.setColor(new Color(156,1,1));
//g.drawLine(0,0,0,20);
/////////////////////////////////////////////////////

[dcaffrey]

Logged In: YES
user_id=1040751
Originator: YES

This bug can be fixed by replacing with Boxlayout with import java.awt.FlowLayout;

Replace:
bottom_panel.setLayout(new BoxLayout(bottom_panel, BoxLayout.Y_AXIS));
with:
FlowLayout myLayout = new FlowLayout();
myLayout.setAlignment(FlowLayout.LEFT);
bottom_panel.setLayout(myLayout);

Comment out:
//bottom_panel.add(consensus_component3);
//bottom_panel.add(consensus_component2);

However this means the top panels need to be changed. This is slightly trickier as they are not all displayed at the same time. Need to modify so only filter or sort but not both are displayed:

//top_panel.setBackground(Color.white);
//top_panel.setLayout(new BoxLayout(top_panel, BoxLayout.Y_AXIS));
GridLayout grid = new GridLayout();
grid.setColumns(1);
grid.setRows(3);
top_panel.setLayout(grid);
FlowLayout topFlow = new FlowLayout();
topFlow.setAlignment(FlowLayout.LEFT);
/*FlowLayout topFlow2 = new FlowLayout();
topFlow2.setAlignment(FlowLayout.LEFT);
FlowLayout topFlow3 = new FlowLayout();
topFlow3.setAlignment(FlowLayout.LEFT);
FlowLayout topFlow4 = new FlowLayout();
topFlow4.setAlignment(FlowLayout.LEFT);
FlowLayout topFlow5 = new FlowLayout();
topFlow5.setAlignment(FlowLayout.LEFT); */

JPanel p1 = new JPanel();
p1.setLayout(topFlow);
JPanel p2 = new JPanel();
p2.setLayout(topFlow);
JPanel p3 = new JPanel();
p3.setLayout(topFlow);
JPanel p4 = new JPanel();
p4.setLayout(topFlow);
JPanel p5 = new JPanel();
p5.setLayout(topFlow);

p4.add(column_filter);
p5.add(column_sort);
top_panel.add(p1);
top_panel.add(p2);
//top_panel.add(p3);
// phdana filter ->
top_panel.add(p4);
//top_panel.add(p5);

p1.add(new ColumnAnnotationComponent(alignment, props));
p2.add(new RulerComponent(alignment, props));
p3.add(new RulerAnnotationComponent(alignment, props,
AlignmentFrame.this));