Methods
Change Log:
+icn3d-2.7.9 was release on August 1, 2019. Fixed the effect of Fog on sticks and spheres.
++ icn3d-2.7.8 was release on July 31, 2019. Fixed SNP annotation in the sequences and annotations window.
diff --git a/package.json b/package.json index 6d044dab..b534571e 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "icn3d", - "version": "2.7.8", + "version": "2.7.9", "description": "iCn3D Structure Viewer", "main": "index.html", "scripts": { diff --git a/src/icn3d/draw/impostor.js b/src/icn3d/draw/impostor.js index 34cf1660..f4fc3f18 100644 --- a/src/icn3d/draw/impostor.js +++ b/src/icn3d/draw/impostor.js @@ -201,6 +201,7 @@ iCn3D.prototype.setParametersForShader = function (opacity) { var me = this; if(this.opts['fog'] === 'yes') { this.defines['USE_FOG'] = 1; + if(this.opts['camera'] === 'orthographic') { this.defines['FOG_EXP2'] = 1; } diff --git a/src/icn3dui/full_ui.js b/src/icn3dui/full_ui.js index 0d592eb7..472e2157 100644 --- a/src/icn3dui/full_ui.js +++ b/src/icn3dui/full_ui.js @@ -15,7 +15,7 @@ if (!$.ui.dialog.prototype._makeDraggableBase) { var iCn3DUI = function(cfg) { var me = this; - this.REVISION = '2.7.8'; + this.REVISION = '2.7.9'; me.bFullUi = true; diff --git a/src/icn3dui/selection/commands.js b/src/icn3dui/selection/commands.js index 4f556f09..5e86aa2a 100644 --- a/src/icn3dui/selection/commands.js +++ b/src/icn3dui/selection/commands.js @@ -1095,7 +1095,7 @@ iCn3DUI.prototype.applyCommand = function (commandStr) { var me = this; var radius = parseFloat(paraArray[0].substr(paraArray[0].lastIndexOf(' ') + 1)); var nameArray = []; - if(paraArray.length == 2) { + if(paraArray.length == 2 && paraArray[1].length > 4) { //sets a,b,c var nameStr = paraArray[1].substr(paraArray[1].indexOf(' ') + 1); nameArray = nameStr.split(","); } @@ -1292,7 +1292,7 @@ iCn3DUI.prototype.applyCommand = function (commandStr) { var me = this; var threshold = parseFloat(paraArray[0].substr(paraArray[0].indexOf(' ') + 1)); var nameArray = []; - if(paraArray.length == 2) { + if(paraArray.length == 2 && paraArray[1].length > 4) { //sets a,b,c var nameStr = paraArray[1].substr(paraArray[1].indexOf(' ') + 1); nameArray = nameStr.split(","); } diff --git a/src/shader/CylinderImpostor.frag b/src/shader/CylinderImpostor.frag index 589a9726..e4eddd5f 100644 --- a/src/shader/CylinderImpostor.frag +++ b/src/shader/CylinderImpostor.frag @@ -294,7 +294,21 @@ $NGL_shaderTextHash['CylinderImpostor.frag'] = ["#define STANDARD", " #include premultiplied_alpha_fragment", " #include tonemapping_fragment", " #include encodings_fragment", -" #include fog_fragment", +" //include fog_fragment", +" #ifdef USE_FOG", +" #ifdef USE_LOGDEPTHBUF_EXT", +" float depth = gl_FragDepthEXT / gl_FragCoord.w;", +" #else", +" float depth = gl_FragCoord.z / gl_FragCoord.w;", +" #endif", +" #ifdef FOG_EXP2", +" float fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );", +" #else", +" float fogFactor = smoothstep( fogNear, fogFar, depth );", +" #endif", +" gl_FragColor.rgb = mix( gl_FragColor.rgb, fogColor, fogFactor );", +" #endif", +"", " #endif", "", "}" diff --git a/src/shader/CylinderImpostor.vert b/src/shader/CylinderImpostor.vert index 766498df..5f857736 100644 --- a/src/shader/CylinderImpostor.vert +++ b/src/shader/CylinderImpostor.vert @@ -37,6 +37,8 @@ $NGL_shaderTextHash['CylinderImpostor.vert'] = ["// Open-Source PyMOL is Copyrig "varying vec3 V;", "varying vec4 w;", "varying float fogDepth;", +"varying float fogNear;", +"varying float fogFar;", "", "#ifdef PICKING", " #include unpack_clr", diff --git a/src/shader/CylinderInstancing.vert b/src/shader/CylinderInstancing.vert index da66ed7e..31866b79 100644 --- a/src/shader/CylinderInstancing.vert +++ b/src/shader/CylinderInstancing.vert @@ -41,6 +41,8 @@ $NGL_shaderTextHash['CylinderInstancing.vert'] = ["// Open-Source PyMOL is Copyr "varying vec3 V;", "varying vec4 w;", "varying float fogDepth;", +"varying float fogNear;", +"varying float fogFar;", "", "#ifdef PICKING", " #include unpack_clr", diff --git a/src/shader/SphereImpostor.frag b/src/shader/SphereImpostor.frag index 99163c09..102feb8c 100644 --- a/src/shader/SphereImpostor.frag +++ b/src/shader/SphereImpostor.frag @@ -162,7 +162,20 @@ $NGL_shaderTextHash['SphereImpostor.frag'] = ["#define STANDARD", " #include premultiplied_alpha_fragment", " #include tonemapping_fragment", " #include encodings_fragment", -" #include fog_fragment", +" //include fog_fragment", +" #ifdef USE_FOG", +" #ifdef USE_LOGDEPTHBUF_EXT", +" float depth = gl_FragDepthEXT / gl_FragCoord.w;", +" #else", +" float depth = gl_FragCoord.z / gl_FragCoord.w;", +" #endif", +" #ifdef FOG_EXP2", +" float fogFactor = whiteCompliment( exp2( - fogDensity * fogDensity * depth * depth * LOG2 ) );", +" #else", +" float fogFactor = smoothstep( fogNear, fogFar, depth );", +" #endif", +" gl_FragColor.rgb = mix( gl_FragColor.rgb, fogColor, fogFactor );", +" #endif", "", " #endif", "", diff --git a/src/shader/SphereImpostor.vert b/src/shader/SphereImpostor.vert index 04993990..4494d907 100644 --- a/src/shader/SphereImpostor.vert +++ b/src/shader/SphereImpostor.vert @@ -6,6 +6,8 @@ $NGL_shaderTextHash['SphereImpostor.vert'] = ["uniform mat4 projectionMatrixInve "varying vec3 vPoint;", "varying vec3 vPointViewPosition;", "varying float fogDepth;", +"varying float fogNear;", +"varying float fogFar;", "", "attribute vec2 mapping;", "//attribute vec3 position;", diff --git a/src/shader/SphereInstancing.vert b/src/shader/SphereInstancing.vert index b6495c33..f78c0b9f 100644 --- a/src/shader/SphereInstancing.vert +++ b/src/shader/SphereInstancing.vert @@ -6,6 +6,8 @@ $NGL_shaderTextHash['SphereInstancing.vert'] = ["uniform mat4 projectionMatrixIn "varying vec3 vPoint;", "varying vec3 vPointViewPosition;", "varying float fogDepth;", +"varying float fogNear;", +"varying float fogFar;", "", "attribute vec2 mapping;", "//attribute vec3 position;",