24 January 2008

Scrollable HTML table

A CSS tip I learned today: you can get a scrollable HTML table by using overflow in the associated CSS stylesheet.



<table style=' width:500px;border-collapse:collapse; font-family: sans-serif;border: 1px solid blue;' >
<thead><tr><th>ACC</th><th>Position</th></tr></thead>
<tbody style="height:105; overflow-y:auto;overflow-x:hidden;">
<tr><td>NP_001004053</td><td><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&p
osition=chr22:14636331-14667937">chr22:14636331-14667937</a></td></tr>
<tr><td>NP_001005239</td><td><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&p
osition=chr22:14828823-14829804">chr22:14828823-14829804</a></td></tr>
<tr><td>Q9UJS3</td><td><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&positio
n=chr22:15451647-15453700">chr22:15451647-15453700</a></td></tr>
<tr><td>Q5GH77</td><td><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&positio
n=chr22:15644305-15682584">chr22:15644305-15682584</a></td></tr>
<tr><td>Q2WGN9</td><td><a href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&positio
n=chr22:15822826-15869112">chr22:15822826-15869112</a></td></tr>
...many rows...
</tbody>
</table>


the result:

shhh... doesn't display correctly within blogger

23 January 2008

Introduction of new relationship types in GO

FYI: via the GO-friends mailing list.
We are pleased to announce that The Gene Ontology Consortium will
introduce three new relationship types


  • regulates

  • negatively_regulates

  • positively_regulates

into the BiologicalProcess ontology.

17 January 2008

Thomson scientific launches www.researcherid.com

http://www.researcherid.com

Thomson scientific launches researcher id.com to associate a researcher with their published works:

Unique Identifier Ensures An Accurate Record Of A Researcher’s Output And Attribution and Builds a World-class Author Community

Researcher ID is a global, multi-disciplinary scholarly research community. Each researcher listed is assigned a unique identifier, to aid in solving the common problem of author misidentification. Search the registry to find citations, collaborators, and more.

see also: http://scientific.thomson.com/press/2008/8429910/

Pierre

14 January 2008

Nucl. Acids Res.: Database issue, January 2008

The annual database issue of NAR is freely available at:http://nar.oxfordjournals.org/content/vol36/suppl_1/index.dtl?etoc

The 2008 update includes 1078 databases, 110 more than the previous one. The links to more than 80 databases have been updated and 25 obsolete databases have been removed from the list.

Who can say: "I'm a specialist in the databases in biology" ?

11 January 2008

Scientists for Better PCR

Via:Coffee and Science.

10 January 2008

JAVA Native Interface (JNI): notebook

The JAVA Native Interface (JNI)allows Java code running in the Java virtual machine to call and (be called) some methods from libraries written in C/C++. I've learned this technology by trying to use the CURSES library (an API allowing the programmer to write text user interfaces in a terminal).

We starts by creating a java class: NCurses.java


1 /* A JNI test */
2 public class NCurses
3 {
4 public NCurses() {}
5 /** initializes the ncurses library */
6 public native static int install();
7 /** disposes the ncurses library */
8 public native static int uninstall();
9 /** set character on screen */
10 public native static void setCharAt(int x,int y,int ch);
11 /** update the screen */
12 public native static void refresh();
13 /** get the number of rows */
14 public native int getRowCount();
15 /** get the number of columns */
16 public native int getColumnCount();
17 /** inverse video */
18 public native int standout();
19 /** normal video */
20 public native int standend();
21
22 /** draw a string at the given position */
23 public void drawString(String s,int x, int y)
24 {
25 int maxx= getColumnCount();
26 for(int i=0;i< s.length() && i+x < maxx;++i)
27 {
28 if(i+3< s.length() && s.substring(i,i+3).equals("<b>"))
29 {
30 standout(); i+=2; continue;
31 }
32 else if(i+4< s.length() && s.substring(i,i+4).equals("</b>"))
33 {
34 standend(); i+=3; continue;
35 }
36 setCharAt(i+x,y,s.charAt(i));
37 }
38 }
39
40 public static void main(String[] args)
41 {
42 //load the C library
43 System.loadLibrary("NCurses");
44 //init curses
45 NCurses.install();
46
47 NCurses sample = new NCurses();
48
49 //draw a box
50 for(int i=1;i+1< sample.getRowCount();++i)
51 {
52 sample.setCharAt(1,i,'*');
53 sample.setCharAt(sample.getColumnCount()-2,i,'*');
54 }
55 for(int i=1;i+1< sample.getColumnCount();++i)
56 {
57 sample.setCharAt(i,1,'*');
58 sample.setCharAt(i,sample.getRowCount()-2,'*');
59 }
60 /* draw some strings */
61 int n=0;
62 for(int i=2;i+3< sample.getRowCount();i+=3)
63 {
64 sample.drawString("<b>Menu \t"+(++n)+"</b>: Hello Menu",5,i);
65 }
66 /* update the screen */
67 sample.refresh();
68 /* wait 10 sec */
69 try{ Thread.sleep(10000); } catch(Exception err) {}
70 //dispose ncurses
71 NCurses.uninstall();
72 }
73 }


This class contains some native methods that are not implemented in this class but they will be loading (line 43 by calling System.loadLibrary)

We can compile this class:
javac NCurses.java


We can run JAVAH on this class. javah will generate the C header file that are needed to implement our native methods.

javah NCurses


This generates the following file: NCurses.h


1 /* DO NOT EDIT THIS FILE - it is machine generated */
2 #include <jni.h>
3 /* Header for class NCurses */
4
5 #ifndef _Included_NCurses
6 #define _Included_NCurses
7 #ifdef __cplusplus
8 extern "C" {
9 #endif
10 /*
11 * Class: NCurses
12 * Method: install
13 * Signature: ()I
14 */
15 JNIEXPORT jint JNICALL Java_NCurses_install
16 (JNIEnv *, jclass);
17
18 /*
19 * Class: NCurses
20 * Method: uninstall
21 * Signature: ()I
22 */
23 JNIEXPORT jint JNICALL Java_NCurses_uninstall
24 (JNIEnv *, jclass);
25
26 /*
27 * Class: NCurses
28 * Method: setCharAt
29 * Signature: (III)V
30 */
31 JNIEXPORT void JNICALL Java_NCurses_setCharAt
32 (JNIEnv *, jclass, jint, jint, jint);
33
34 /*
35 * Class: NCurses
36 * Method: refresh
37 * Signature: ()V
38 */
39 JNIEXPORT void JNICALL Java_NCurses_refresh
40 (JNIEnv *, jclass);
41
42 /*
43 * Class: NCurses
44 * Method: getRowCount
45 * Signature: ()I
46 */
47 JNIEXPORT jint JNICALL Java_NCurses_getRowCount
48 (JNIEnv *, jobject);
49
50 /*
51 * Class: NCurses
52 * Method: getColumnCount
53 * Signature: ()I
54 */
55 JNIEXPORT jint JNICALL Java_NCurses_getColumnCount
56 (JNIEnv *, jobject);
57
58 /*
59 * Class: NCurses
60 * Method: standout
61 * Signature: ()I
62 */
63 JNIEXPORT jint JNICALL Java_NCurses_standout
64 (JNIEnv *, jobject);
65
66 /*
67 * Class: NCurses
68 * Method: standend
69 * Signature: ()I
70 */
71 JNIEXPORT jint JNICALL Java_NCurses_standend
72 (JNIEnv *, jobject);
73
74 #ifdef __cplusplus
75 }
76 #endif
77 #endif


I've implemented the C methods in the following file: NCurses.c

1 #include "NCurses.h"
2 #include <string.h>
3 #include <curses.h>
4 #include <signal.h>
5
6 JNIEXPORT jint JNICALL Java_NCurses_install(JNIEnv *env, jclass clazz)
7 {
8 //(void) signal(SIGINT, finish); /* arrange interrupts to terminate */
9
10 (void) initscr(); /* initialize the curses library */
11 keypad(stdscr, TRUE); /* enable keyboard mapping */
12 (void) nonl(); /* tell curses not to do NL->CR/NL on output */
13 (void) cbreak(); /* take input chars one at a time, no wait for \n */
14 (void) noecho(); /* don't echo input */
15 clear();
16 move(0,0);
17 refresh();
18 return 0;
19 }
20
21 JNIEXPORT jint JNICALL Java_NCurses_uninstall(JNIEnv *env, jclass clazz)
22 {
23 endwin();
24 return 0;
25 }
26
27 JNIEXPORT jint JNICALL Java_NCurses_getRowCount(JNIEnv *env, jobject obj)
28 {
29 int h, w;
30 getmaxyx(stdscr, h, w);
31 return h;
32 }
33
34
35 JNIEXPORT jint JNICALL Java_NCurses_getColumnCount(JNIEnv *env, jobject obj)
36 {
37 int h, w;
38 getmaxyx(stdscr, h, w);
39 return w;
40 }
41
42 /*
43 * Class: NCurses
44 * Method: setCharAt
45 * Signature: (III)V
46 */
47 JNIEXPORT void JNICALL Java_NCurses_setCharAt
48 (JNIEnv *env, jclass object, jint x, jint y, jint chr)
49 {
50 mvaddch(y,x,chr);
51 }
52
53 /*
54 * Class: NCurses
55 * Method: refresh
56 * Signature: ()V
57 */
58 JNIEXPORT void JNICALL Java_NCurses_refresh
59 (JNIEnv *env, jclass object)
60 {
61 refresh();
62 }
63
64
65 /*
66 * Class: NCurses
67 * Method: standout
68 * Signature: ()I
69 */
70 JNIEXPORT jint JNICALL Java_NCurses_standout
71 (JNIEnv *env, jobject object)
72 {
73 standout();
74 }
75
76 /*
77 * Class: NCurses
78 * Method: standend
79 * Signature: ()I
80 */
81 JNIEXPORT jint JNICALL Java_NCurses_standend
82 (JNIEnv * env, jobject object)
83 {
84 standend();
85 }


before compiling the C source, I set the variable LD_LIBRARY_PATH. For my machine it was:
export LD_LIBRARY_PATH=${PWD}:/usr/local/lib:/usr/lib


We can now compile NCurses.c and create the C library. You may need to add the path the java C headers which are contained in ${JAVA_HOME}/include/ and ${JAVA_HOME}/include/{your-machine}

gcc -fpic -c NCurses.c -o NCurses.o
gcc -shared -o libNCurses.so NCurses.o -lcurses


Let's run our java program:

java NCurses


The result looks like this:

*********************************************
* Menu 1 : Hello Menu *
* *
* *
* Menu 2 : Hello Menu *
* *
* *
* Menu 3 : Hello Menu *
* *
* *
* Menu 4 : Hello Menu *
* *
* *
* Menu 5 : Hello Menu *
* *
* *
* Menu 6 : Hello Menu *
* *
* *
* *
*********************************************


That's it.
Pierre