AlignmentCalc

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Summary:
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Constr |
Method

Detail:
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Constr |
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java.lang.Object
- org.biojava.nbio.structure.gui.util.AlignmentCalc

All Implemented Interfaces:

java.lang.Runnable
```
public class AlignmentCalc
extends java.lang.Object
implements java.lang.Runnable
```
A class that obtains two structures via DAS and aligns them This is done in a separate thread. It is possible to register Event listeners to get notification of when the download has finished.

Since:

1.7

Version:

%I% %G%

Author:

Andreas Prlic

Constructor Summary

Constructors
Constructor Description

AlignmentCalc(AlignmentGui parent, Structure s1, Structure s2)
requests an alignment of pdb1 vs pdb 2.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`cleanup()`
`void`	`interrupt()`	stops what is currently happening and does not continue
`void`	`run()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - AlignmentCalc
```
public AlignmentCalc(AlignmentGui parent,
                     Structure s1,
                     Structure s2)
```
    requests an alignment of pdb1 vs pdb 2. Chain 1 and chain2 are optional. If they are empty strings, they are ignored
    
    Parameters:
    
    parent - the alignment gui frame that interacts with this class
    
    s1 - structure 1
    
    s2 - structure 2
- Method Detail
  - run
```
public void run()
```
    Specified by:
    
    run in interface java.lang.Runnable
  - interrupt
```
public void interrupt()
```
    stops what is currently happening and does not continue
  - cleanup
```
public void cleanup()
```

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